From 95942ac299ceed2cebad455397574999190407f3 Mon Sep 17 00:00:00 2001 From: cmungall Date: Thu, 14 Mar 2024 01:38:32 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20INCATool?= =?UTF-8?q?s/ontology-access-kit@e76ee10015f36bfad4c00c2c5e5f04c3a3a8518f?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../association_provider_interface.html | 100 ++++++++-- .../ClassEnrichmentResult.md.txt | 4 +- .../class-enrichment/p_value.md.txt | 3 - _sources/howtos/use-llms.rst.txt | 2 + _sources/packages/implementations/llm.rst.txt | 17 +- class-enrichment/ClassEnrichmentResult.md | 4 +- class-enrichment/p_value.md | 3 - cli.html | 171 +++++++++++++++++- .../ClassEnrichmentResult.html | 4 +- datamodels/class-enrichment/p_value.html | 2 - genindex.html | 125 +++++++++++++ objects.inv | Bin 48884 -> 49081 bytes packages/implementations/index.html | 1 + packages/implementations/llm.html | 14 ++ packages/interfaces/association-provider.html | 65 +++++-- packages/interfaces/index.html | 1 + searchindex.js | 2 +- 17 files changed, 460 insertions(+), 58 deletions(-) diff --git a/_modules/oaklib/interfaces/association_provider_interface.html b/_modules/oaklib/interfaces/association_provider_interface.html index 4a6062c77..1dd516d88 100644 --- a/_modules/oaklib/interfaces/association_provider_interface.html +++ b/_modules/oaklib/interfaces/association_provider_interface.html @@ -519,6 +519,66 @@

Source code for oaklib.interfaces.association_provider_interface

return True
+
+[docs] + def association_counts( + self, + subjects: Iterable[CURIE] = None, + predicates: Iterable[PRED_CURIE] = None, + property_filter: Dict[PRED_CURIE, Any] = None, + subject_closure_predicates: Optional[List[PRED_CURIE]] = None, + predicate_closure_predicates: Optional[List[PRED_CURIE]] = None, + object_closure_predicates: Optional[List[PRED_CURIE]] = None, + include_modified: bool = False, + group_by: Optional[str] = "object", + limit: Optional[int] = None, + **kwargs, + ) -> Iterator[Tuple[CURIE, int]]: + """ + Yield objects together with the number of distinct associations. + + :param subjects: + :param predicates: + :param property_filter: + :param subject_closure_predicates: + :param predicate_closure_predicates: + :param object_closure_predicates: + :param include_modified: + :param group_by: + :param limit: + :param kwargs: + :return: + """ + association_it = self.associations( + subjects=subjects, + predicates=predicates, + property_filter=property_filter, + subject_closure_predicates=subject_closure_predicates, + predicate_closure_predicates=predicate_closure_predicates, + include_modified=include_modified, + **kwargs, + ) + assoc_map = defaultdict(list) + cached = {} + if isinstance(self, OboGraphInterface): + for association in association_it: + if group_by == "object": + grp = association.object + if grp not in cached: + grps = list(self.ancestors([grp], predicates=object_closure_predicates)) + cached[grp] = grps + else: + grps = cached[grp] + elif group_by == "subject": + grps = [association.subject] + else: + raise ValueError(f"Unknown group_by: {group_by}") + for grp in grps: + assoc_map[grp].append(association) + for k, v in assoc_map.items(): + yield k, len(v)
+ +
[docs] def association_subject_counts( @@ -530,6 +590,7 @@

Source code for oaklib.interfaces.association_provider_interface

predicate_closure_predicates: Optional[List[PRED_CURIE]] = None, object_closure_predicates: Optional[List[PRED_CURIE]] = None, include_modified: bool = False, + **kwargs, ) -> Iterator[Tuple[CURIE, int]]: """ Yield objects together with the number of distinct associated subjects. @@ -549,15 +610,17 @@

Source code for oaklib.interfaces.association_provider_interface

GO:0051668 3 ... - This shows that GO:0051668 (localization within membrane) is used for all 3 input subjects + This shows that GO:0051668 (localization within membrane) is used for all 3 input subjects. + If subjects is empty, this is calculated for all subjects in the association set. - :param subjects: - :param predicates: - :param property_filter: - :param subject_closure_predicates: - :param predicate_closure_predicates: - :param object_closure_predicates: - :param include_modified: + :param subjects: constrain to these subjects (e.g. genes in a gene association) + :param predicates: constrain to these predicates (e.g. involved-in for a gene to pathway association) + :param property_filter: generic filter + :param subject_closure_predicates: subjects is treated as descendant via these predicates + :param predicate_closure_predicates: predicates is treated as descendant via these predicates + :param object_closure_predicates: object is treated as descendant via these predicates + :param include_modified: include modified associations + :param kwargs: additional arguments :return: """ association_it = self.associations( @@ -567,6 +630,7 @@

Source code for oaklib.interfaces.association_provider_interface

subject_closure_predicates=subject_closure_predicates, predicate_closure_predicates=predicate_closure_predicates, include_modified=include_modified, + **kwargs, ) object_to_subject_map = defaultdict(set) cached = {} @@ -603,16 +667,16 @@

Source code for oaklib.interfaces.association_provider_interface

""" Maps matching associations to a subset (map2slim, rollup). - :param subjects: - :param predicates: - :param objects: - :param subset: - :param subset_entities: - :param property_filter: - :param subject_closure_predicates: - :param predicate_closure_predicates: - :param object_closure_predicates: - :param include_modified: + :param subjects: constrain to these subjects + :param predicates: constrain to these predicates (e.g. involved-in for a gene to pathway association) + :param objects: constrain to these objects (e.g. terms) + :param subset: subset to map to + :param subset_entities: subset entities to map to + :param property_filter: generic filter + :param subject_closure_predicates: subjects is treated as descendant via these predicates + :param predicate_closure_predicates: predicates is treated as descendant via these predicates + :param object_closure_predicates: object is treated as descendant via these predicates + :param include_modified: include modified associations :return: """ # Default implementation: this may be overridden for efficiency diff --git a/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt b/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt index fcbdfef9a..83b645c0d 100644 --- a/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt +++ b/_sources/datamodels/class-enrichment/ClassEnrichmentResult.md.txt @@ -61,7 +61,7 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl | [class_id](class_id.md) | 1..1
[Uriorcurie](Uriorcurie.md) | The class id | direct | | [class_label](class_label.md) | 0..1
[String](String.md) | The class label | direct | | [rank](rank.md) | 0..1
[Integer](Integer.md) | The rank of this result | direct | -| [p_value](p_value.md) | 1..1
[Float](Float.md) | The p-value | direct | +| [p_value](p_value.md) | 0..1
[Float](Float.md) | The p-value | direct | | [p_value_adjusted](p_value_adjusted.md) | 0..1
[Float](Float.md) | The adjusted p-value | direct | | [false_discovery_rate](false_discovery_rate.md) | 0..1
[Float](Float.md) | The false discovery rate | direct | | [fold_enrichment](fold_enrichment.md) | 0..1
[Float](Float.md) | The fold enrichment | direct | @@ -163,7 +163,6 @@ attributes: domain_of: - ClassEnrichmentResult range: float - required: true p_value_adjusted: name: p_value_adjusted description: The adjusted p-value @@ -308,7 +307,6 @@ attributes: domain_of: - ClassEnrichmentResult range: float - required: true p_value_adjusted: name: p_value_adjusted description: The adjusted p-value diff --git a/_sources/datamodels/class-enrichment/p_value.md.txt b/_sources/datamodels/class-enrichment/p_value.md.txt index e22056887..61f70a30f 100644 --- a/_sources/datamodels/class-enrichment/p_value.md.txt +++ b/_sources/datamodels/class-enrichment/p_value.md.txt @@ -30,8 +30,6 @@ URI: [OBI:0000175](http://purl.obolibrary.org/obo/OBI_0000175) * Range: [Float](Float.md) -* Required: True - @@ -66,7 +64,6 @@ owner: ClassEnrichmentResult domain_of: - ClassEnrichmentResult range: float -required: true ``` \ No newline at end of file diff --git a/_sources/howtos/use-llms.rst.txt b/_sources/howtos/use-llms.rst.txt index 415b88b32..c08950829 100644 --- a/_sources/howtos/use-llms.rst.txt +++ b/_sources/howtos/use-llms.rst.txt @@ -1,3 +1,5 @@ +.. _use_llms + How to use Large Language Models (LLMs) with OAK =============================================== diff --git a/_sources/packages/implementations/llm.rst.txt b/_sources/packages/implementations/llm.rst.txt index dfe361a63..815039767 100644 --- a/_sources/packages/implementations/llm.rst.txt +++ b/_sources/packages/implementations/llm.rst.txt @@ -3,6 +3,8 @@ LLM Adapter ============= +See also :ref:`use_llms` + Command Line Examples ---------------------- @@ -14,12 +16,25 @@ Use the :code:`llm` selector, wrapping an existing source Annotation ^^^^^^^^^^ + .. code:: shell runoak -i llm:sqlite:obo:hp annotate "abnormalities were found in the eye and the liver" +Validation of Mappings +^^^^^^^^^^^^^^^^^^^^^^ + +.. code:: shell + + runoak -i llm:sqlite:obo:go validate-mappings .desc//p=i "molecular_function" + +See: + + - `MapperGPT `_ + - `GO RHEA Analysis `_ + Code ---- -.. currentmodule:: oaklib.implementations.llm +.. currentmodule:: oaklib.implementations.llm.llm_implementation .. autoclass:: LLMImplementation diff --git a/class-enrichment/ClassEnrichmentResult.md b/class-enrichment/ClassEnrichmentResult.md index fcbdfef9a..83b645c0d 100644 --- a/class-enrichment/ClassEnrichmentResult.md +++ b/class-enrichment/ClassEnrichmentResult.md @@ -61,7 +61,7 @@ URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/Cl | [class_id](class_id.md) | 1..1
[Uriorcurie](Uriorcurie.md) | The class id | direct | | [class_label](class_label.md) | 0..1
[String](String.md) | The class label | direct | | [rank](rank.md) | 0..1
[Integer](Integer.md) | The rank of this result | direct | -| [p_value](p_value.md) | 1..1
[Float](Float.md) | The p-value | direct | +| [p_value](p_value.md) | 0..1
[Float](Float.md) | The p-value | direct | | [p_value_adjusted](p_value_adjusted.md) | 0..1
[Float](Float.md) | The adjusted p-value | direct | | [false_discovery_rate](false_discovery_rate.md) | 0..1
[Float](Float.md) | The false discovery rate | direct | | [fold_enrichment](fold_enrichment.md) | 0..1
[Float](Float.md) | The fold enrichment | direct | @@ -163,7 +163,6 @@ attributes: domain_of: - ClassEnrichmentResult range: float - required: true p_value_adjusted: name: p_value_adjusted description: The adjusted p-value @@ -308,7 +307,6 @@ attributes: domain_of: - ClassEnrichmentResult range: float - required: true p_value_adjusted: name: p_value_adjusted description: The adjusted p-value diff --git a/class-enrichment/p_value.md b/class-enrichment/p_value.md index e22056887..61f70a30f 100644 --- a/class-enrichment/p_value.md +++ b/class-enrichment/p_value.md @@ -30,8 +30,6 @@ URI: [OBI:0000175](http://purl.obolibrary.org/obo/OBI_0000175) * Range: [Float](Float.md) -* Required: True - @@ -66,7 +64,6 @@ owner: ClassEnrichmentResult domain_of: - ClassEnrichmentResult range: float -required: true ``` \ No newline at end of file diff --git a/cli.html b/cli.html index 0654f4c00..8a4bb3d3f 100644 --- a/cli.html +++ b/cli.html @@ -69,6 +69,7 @@
  • apply-obsolete
  • apply-taxon-constraints
  • associations
    • +
  • associations-counts
  • associations-matrix
  • axioms
  • cache-clear
    • @@ -1032,6 +1033,157 @@

    associations +

    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

    @@ -1979,6 +2131,12 @@

    enrichment +
    +--allow-labels, --no-allow-labels
    +

    If true, allow labels as well as CURIEs in the input files

    +
    +

    Arguments

    @@ -5460,16 +5618,25 @@

    validate-mappings

    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.

    -

    You can customize this:

    +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]...
    diff --git a/datamodels/class-enrichment/ClassEnrichmentResult.html b/datamodels/class-enrichment/ClassEnrichmentResult.html index 9566b8a1c..39853a653 100644 --- a/datamodels/class-enrichment/ClassEnrichmentResult.html +++ b/datamodels/class-enrichment/ClassEnrichmentResult.html @@ -149,7 +149,7 @@

    Slots

    direct

    p_value

    -

    1..1
    Float

    +

    0..1
    Float

    The p-value

    direct

    @@ -302,7 +302,6 @@

    Direct< domain_of: - ClassEnrichmentResult range: float - required: true p_value_adjusted: name: p_value_adjusted description: The adjusted p-value @@ -445,7 +444,6 @@

    Direct< domain_of: - ClassEnrichmentResult range: float - required: true p_value_adjusted: name: p_value_adjusted description: The adjusted p-value diff --git a/datamodels/class-enrichment/p_value.html b/datamodels/class-enrichment/p_value.html index 4c97eeba4..2bd3d9f32 100644 --- a/datamodels/class-enrichment/p_value.html +++ b/datamodels/class-enrichment/p_value.html @@ -109,7 +109,6 @@

    Applicable Classes

    • Range: Float

      • -

    • Required: True

    @@ -135,7 +134,6 @@

    LinkML Source
    </details>

    diff --git a/genindex.html b/genindex.html index bcb7df277..e22819c15 100644 --- a/genindex.html +++ b/genindex.html @@ -139,6 +139,8 @@

    Symbols
  • @@ -182,6 +184,13 @@

    Symbols

    • +
  • + --allow-labels + +
  • @@ -221,6 +230,8 @@

    Symbols

    • runoak-associations command line option +
      • +
    • runoak-associations-counts command line option
    • runoak-associations-matrix command line option
      • @@ -248,6 +259,8 @@

      Symbols

      +
    • + --limit + +
    • @@ -897,6 +926,13 @@

      Symbols

      • +
    • + --min-facet-count + +
    • @@ -962,6 +998,8 @@

      Symbols

    • @@ -1005,6 +1043,13 @@

      Symbols

      • +
    • + --no-allow-labels + +
    • @@ -1044,6 +1089,8 @@

      Symbols

      • runoak-associations command line option +
        • +
      • runoak-associations-counts command line option
      • runoak-associations-matrix command line option
        • @@ -1602,6 +1649,8 @@

        Symbols

      • runoak-apply-taxon-constraints command line option
      • runoak-associations command line option, [1] +
        • +
      • runoak-associations-counts command line option, [1]
      • runoak-associations-matrix command line option, [1]
        • @@ -1739,6 +1788,8 @@

        Symbols

      • runoak-apply-obsolete command line option
      • runoak-associations command line option +
        • +
      • runoak-associations-counts command line option
      • runoak-associations-matrix command line option
        • @@ -1906,6 +1957,8 @@

        Symbols

      • runoak-apply-taxon-constraints command line option
      • runoak-associations command line option +
        • +
      • runoak-associations-counts command line option
      • runoak-associations-matrix command line option
        • @@ -2223,6 +2276,8 @@

        Symbols

        • runoak-associations command line option +
          • +
        • runoak-associations-counts command line option
        • runoak-associations-matrix command line option
          • @@ -2368,6 +2423,13 @@

          Symbols

          +
        • + -F + +
        • @@ -2405,6 +2467,8 @@

          Symbols

          • runoak-annotate command line option +
            • +
          • runoak-associations-counts command line option
          • runoak-lexmatch command line option
            • @@ -2459,6 +2523,8 @@

            Symbols

          • runoak-apply-obsolete command line option
          • runoak-associations command line option +
            • +
          • runoak-associations-counts command line option
          • runoak-associations-matrix command line option
            • @@ -2572,6 +2638,8 @@

            Symbols

          • runoak-apply-taxon-constraints command line option
          • runoak-associations command line option, [1] +
            • +
          • runoak-associations-counts command line option, [1]
          • runoak-associations-matrix command line option, [1]
            • @@ -2714,6 +2782,8 @@

            Symbols

          • runoak-apply-taxon-constraints command line option
          • runoak-associations command line option +
            • +
          • runoak-associations-counts command line option
          • runoak-associations-matrix command line option
            • @@ -2771,6 +2841,8 @@

            Symbols

            +
          • + runoak-associations-counts command line option + +
          • @@ -4306,6 +4425,8 @@

            R

            runoak-enrichment command line option
              +
            • --allow-labels +
            • --association-predicates
            • --autolabel @@ -4315,6 +4436,8 @@

              R

            • --cutoff
            • --filter-redundant +
              • +
            • --no-allow-labels
            • --no-autolabel
              • @@ -5721,6 +5844,8 @@

              T

            • runoak-apply-obsolete command line option
            • runoak-associations command line option +
              • +
            • runoak-associations-counts command line option
            • runoak-associations-matrix command line option
              • diff --git a/objects.inv b/objects.inv index 7e17accac66d2d64445969c3473f845934d1fb3b..8cd4d89cdb92034acf23b9d0f54ebc1560103783 100644 GIT binary patch delta 48963 zcmV)IK)k>7{Q|lF0+4rqavV95Ci0O;z_ykCh!eZ4#wYaa(G#MOOFN zu{MhdW(LV9MMk6|B6;aw`x^Ut`y`7y;D7^gBq>qnN0pd>fBt#gaB(;sWAmx+E?=z2 z;kKQYcA8&onx(0?MEhGTE=R9|AfrsPvi@lKzcO~<-fY=Ce(tTe>wSh*aP4ypO~M)H*MKH_%c=;@G^V} zL&{%?A}jb0)*@}21+|6!^|Pow?ETkuYelojwe|IH%tNF#;Hq-h>XdXBFzFqy>N)}b~!>}}}A(eGiO2vzF@eecks=MA# z&C-p7`&l4blj_z}+bnG@fAQM{)n4s~wfMV0^U~fgbu$d((k$cj;)4BrC4YIgntR&~ z?7m(#YxXAxR~GEkblY9uZredBn_o27*He2fMD3q7f0TOh%G8{I3fvaR@X}$(8N+VY zc-O0cd?S9|52tti0R||oIr8hS-!w1Y@&6w{BGEYx_O6Tf-u&TTr2e=Lu)yff8qtgY z0_uJ~gq11F5)R9F*|z%MfLInELar2N4Y*_D;|KLmKrc!UVV7ESXH~Rz*FvDuio3d-B z&%OF5utAg_Vt~||CI8&BM>QkFhp`HEPe-b{GrR{sjC_CDPO@P#fB9y7YPyz;a6R8z(YtFV)|t^(4EJ1ClEFJe`apGP0RXOUH{^htv*w=C%Q7%phoo4t726hvnNfZ`X9wT{m;D+W#+Z=e)oCtz9qQ_-*}m4Kp{; znaF(0c79uTa@*{_-BxGdlh?lcXX~2y?OXWtH}SHWyLHWngZ+5@;28IsSDdPHaud-3$f^j$O8{KdX}sKo-yGuhD2&uT$mvw>8% zC=2H2F=4!%$G%>F3)!t_H1^{Z^M1v+;`)4jxMZy zX)EUDwtW`zb+f){>wX+R?RU>}`RjfhIG&+7T8~>kubZEP*;%5|ozqt%mp*LS5I@7U zi|_*W)v@EMZ^nRU^i=Tp7B*0Qmd<}>LEJL4X4jWLD5C#~3OADUu2Cx@S>=1sM zuU$mM)$PE(qZ_^?!R~Co-pfwavE`VHy){zDR)`#5C+aH8^mVMV8|M0}vT(#_vR5i; zH?`2&KCPXb?&=D}alR1+#h54CVaY2K+grf77uHZ zw%dj<33vj&$E{y~5e(RGchCS)Kz~t%_+uE#Uew3a#dlagEzcvLT-E?JBE^EnKgg=$ z4M$2PDJc8^dKm@Ex`r)%JpaW_DtP(6v@NO!)lvPjQ=|AezO-SFdzHVmb$sa*zE$)| z+SjmcnVMnlmhQIw1`RY@NWL9Q)H?XH8}yB}RN*T=kNatV{j?9x<}Wb3CUpU|7l|h< zDC3d)dZ?bpr(+$MC{LClM87`o{1qwZTFZSs(oH+B+hNlTYSZbnFhAQhf5oS}>E`CL zZ{7Y!tX5Tj;42ACeKP*LrvFs$cQD%Hi#~)4eUqa(+zuw=S;y?P-u3jcES6x5qWDE) zGP`kacst3zi2dE+tel|kSkHPn?w2o4#3pL()bfFU>ldUl;|HEws&tjI{(L{D(u+U24Q$rMy|(OK9j@E2blre+{z|0X^)OC+ z|08S3J3#(*ZnO*{Cubaa8q%rdBd7K&-)d4&+|y9)ht2pDRC+X9`-4xAs*v0wX?0b0 z2wF&7v@Z4KtT20u58Ms)6)Zb27W^w%2B)xpm+f-bw!?E8_NY}nx?L(|wzVgdnHytM zNw~{d$e-@x8H&EqC!mw@Ys5T*Pr&!M_vHx;5IfUE7||16^p*|c0q3?E*hJ;L+jf03 zb<0D+8ziCCY_Ly7Eg~f@`QH8BW)!tFgd6eYOcTy)-XqB5{xT;kt7Q{(6|0bcHNK#K zb>nu+9WCU=v@dB4U;Rh!)3e%yJ-2zyhRn}8{+C-sagY!@SDUG=1 zD=1xY4os>IA{1Dp8j>DQV2r3dH+2PnZ=yg}R_zxs;>G2}KFFIogcEMg*Rb!pA1|B! z+qKW^P&e-2Z`RZRSM!*ZsoRm##Fg0y&pC2e`0R;CBfVA5oqTjKv0kHVdGnC>WPJrY zmgaKLI=gSj9#;R1cF26Sn~n`4Sos5``}%Um^zFR}Eisw(p3jtN-}3_|`o3L%>(BS; zj1hiw&yK(8GV(`jv^<`wXe9NNypJ15J*6ex%pUg*Uuw^Pj!(%uwS02%RVjtPN2SQS z>lo>NDT?NLN?Z1Wvv^M4C-{^WD6#fgNa?ZfarU|GMdJ-lcr+?>?HoJiQ465w6FFxv z#x!E8xL1Y^+jc4`_an5x1EW-be5(i;n_0)TZJ$=XRD3f|%MELZ9;th3!*Q_ydkZipV1x^3*0+j~C4aj1ZV7QhWVh%zd}rvUz z`{}|cB=>5jMb*ya1GU@}#}7ID+&3@O-*461UwWt@rb?|{KB3BUkb}8Y;Vb1ZT+Peo zCq6V-RX?n*`*EHdeMBcOt)#3uOSee+Oeb8VphPHVyCKS&Q=R{59k>+qcr=}Rq z{%VK~;-B9glis2CBE=X*Q0}f-y|D*OWKarGIf&{=ZE>YA{-xQrRJqOSWY~1K-DaPE zGlhKR$TJmu_YQ&T^!4fLXYm%~q?u%;BqdCI4>JX(BpK}eImswmYr)0n-6WH)9BBp@ zF~KAvDM{=oq;#c!r8T^yZRhEm-kn`gMbF4Rtvbb=Dk_$@N@U;4Rx5jplzgS-9Tmj4 zQERZTq*frCb#}XdQw~L{D%rq0!0PC%nU>XQw&&zx6%*qC9*Ir3WoJ{n>3BXenlN8% zBubLsvX5_mCW)z?33ORvbNI2n;*+=AmL@D`nJZHFuBGLFGj-s6l3GG1Pou9q>_*YU>c1{#KKR^9I5>x>PD}rJzTX9(zY6CFH8Z3k<+LIetElO-*mAKQy z%7tYG+J`$CXyh#O_kL2N-Gv~+M{NFbIU`I*xXA7lBNv)K`B&_N4#Gknt{>E7lvP?;#gtV>S!I;HqS6`z zS*`YV)1J2lLgSc0TG1=3`;{zm=sdsm<5@j@7`Zy*3c1y)%DlTulKZ;P?VzV7>m-<;L1 z-(Pp$t-cxWmT`V5l{A$UQTkcCA(5(>HN~DTroHJO=59un>Lns}_0@PeRywlF+-3!q zTK>sjOqH5pb^-TL=Y(B}JK!sM2CFx(#j*Td8+R3_4ZGY(~^K9H`ryCaJ^AcGAl}UR-3U(KE z-Re{OFcZza)c#I&uXkM~(67!;R)1!H9Py2s>`C%{%X;ZGX1aPEnO^5lxGz|kU!Qkhyoc(Bh4RwygSi&gd+U*2cz0b9^KhIprh_#b zJcNL?O%E&mrpw-g@%#zuy=p$cyl&YP#yp;hHAEcFzIb*G8ZNpi24`Gx^{21?{3nN> zU6{y=qZ^!gHD2*{WyR)e`?)Q%Mk~{Q?b%$7R~1uMEn~%$dA8-KrKO(V9(&;&8TW6y zaN#P^iPu&g@bn>{h+R>4@Lu9JtfsP>-BkyjL~dnVjPT<2JN^YSv-mwnJ3ME_J!DsS zMlNqNuA1Fbmler*_f6c5nRfl(yDDWrf6QALHZTNjp)a&nLeYkpaKq(TLusmiTusF` zRiYKAG(9e8+puxUJpm;16lCQt*`vOmm?ay^Ao=^%Ya@RoHpB5@@0MR~-wo!QMmqM* zer>-_fvgm=;z-?gtVAOC)v;3go-2JTs|=r5%}Ng*euO*

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              • LLM Adapter
    • -

    This shows that GO:0051668 (localization within membrane) is used for all 3 input subjects

    +

    This shows that GO:0051668 (localization within membrane) is used for all 3 input subjects. +If subjects is empty, this is calculated for all subjects in the association set.

    Parameters:
      -

    • subjects –

      • -

    • predicates –

      • -

    • property_filter –

      • -

    • subject_closure_predicates –

      • -

    • predicate_closure_predicates –

      • -

    • object_closure_predicates –

      • -

    • include_modified –

      • +

    • subjects – constrain to these subjects (e.g. genes in a gene association)

      • +

    • predicates – constrain to these predicates (e.g. involved-in for a gene to pathway association)

      • +

    • property_filter – generic filter

      • +

    • subject_closure_predicates – subjects is treated as descendant via these predicates

      • +

    • predicate_closure_predicates – predicates is treated as descendant via these predicates

      • +

    • object_closure_predicates – object is treated as descendant via these predicates

      • +

    • include_modified – include modified associations

      • +

    • kwargs – additional arguments

    Returns:
    @@ -368,16 +395,16 @@

    Command Line Use
    Parameters:
      -

    • subjects –

      • -

    • predicates –

      • -

    • objects –

      • -

    • subset –

      • -

    • subset_entities –

      • -

    • property_filter –

      • -

    • subject_closure_predicates –

      • -

    • predicate_closure_predicates –

      • -

    • object_closure_predicates –

      • -

    • include_modified –

      • +

    • subjects – constrain to these subjects

      • +

    • predicates – constrain to these predicates (e.g. involved-in for a gene to pathway association)

      • +

    • objects – constrain to these objects (e.g. terms)

      • +

    • subset – subset to map to

      • +

    • subset_entities – subset entities to map to

      • +

    • property_filter – generic filter

      • +

    • subject_closure_predicates – subjects is treated as descendant via these predicates

      • +

    • predicate_closure_predicates – predicates is treated as descendant via these predicates

      • +

    • object_closure_predicates – object is treated as descendant via these predicates

      • +

    • include_modified – include modified associations

    Returns:
    diff --git a/packages/interfaces/index.html b/packages/interfaces/index.html index 122755998..09d4b162f 100644 --- a/packages/interfaces/index.html +++ b/packages/interfaces/index.html @@ -379,6 +379,7 @@
  • AssociationProviderInterface.associations_subject_search()
  • AssociationProviderInterface.association_pairwise_coassociations()
  • AssociationProviderInterface.add_associations()
    • +
  • AssociationProviderInterface.association_counts()
  • AssociationProviderInterface.association_subject_counts()
  • AssociationProviderInterface.map_associations()
  • AssociationProviderInterface.normalize_associations()
    • diff --git a/searchindex.js b/searchindex.js index 5de4bf070..8e682b6ad 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["cli", "concepts", "contributing", "datamodels/association/Association", "datamodels/association/AssociationChange", "datamodels/association/Boolean", "datamodels/association/Curie", "datamodels/association/Date", "datamodels/association/DateOrDatetime", "datamodels/association/Datetime", "datamodels/association/Decimal", "datamodels/association/Double", "datamodels/association/Float", "datamodels/association/Integer", "datamodels/association/Jsonpath", "datamodels/association/Jsonpointer", "datamodels/association/Ncname", "datamodels/association/NegatedAssociation", "datamodels/association/Nodeidentifier", "datamodels/association/Objectidentifier", "datamodels/association/PairwiseCoAssociation", "datamodels/association/ParserConfiguration", "datamodels/association/PositiveOrNegativeAssociation", "datamodels/association/PropertyValue", "datamodels/association/RollupGroup", "datamodels/association/Sparqlpath", "datamodels/association/String", "datamodels/association/Time", "datamodels/association/Uri", "datamodels/association/Uriorcurie", "datamodels/association/aggregator_knowledge_source", "datamodels/association/association", "datamodels/association/associations", "datamodels/association/associations_for_subjects_in_common", "datamodels/association/closure_delta", "datamodels/association/closure_information_content_delta", "datamodels/association/closure_predicates", "datamodels/association/comments", "datamodels/association/core_triple", "datamodels/association/creation_date", "datamodels/association/date", "datamodels/association/denormalized_slot", "datamodels/association/diff_slot", "datamodels/association/evidence_type", "datamodels/association/group_object", "datamodels/association/include_association_attributes", "datamodels/association/index", "datamodels/association/is_creation", "datamodels/association/is_deletion", "datamodels/association/is_generalization", "datamodels/association/is_migration", "datamodels/association/is_specialization", "datamodels/association/modification_date", "datamodels/association/negated", "datamodels/association/new_date", "datamodels/association/new_object", "datamodels/association/new_predicate", "datamodels/association/number_subject_unique_to_entity1", "datamodels/association/number_subject_unique_to_entity2", "datamodels/association/number_subjects_in_common", "datamodels/association/object", "datamodels/association/object1", "datamodels/association/object1_label", "datamodels/association/object2", "datamodels/association/object2_label", "datamodels/association/object_closure", "datamodels/association/object_closure_label", "datamodels/association/object_label", "datamodels/association/old_date", "datamodels/association/old_object", "datamodels/association/old_object_obsolete", "datamodels/association/old_predicate", "datamodels/association/original_object", "datamodels/association/original_predicate", "datamodels/association/original_subject", "datamodels/association/predicate", "datamodels/association/predicate_label", "datamodels/association/preserve_negated_associations", "datamodels/association/primary_knowledge_source", "datamodels/association/property_values", "datamodels/association/publication_is_added", "datamodels/association/publication_is_deleted", "datamodels/association/publications", "datamodels/association/sub_groups", "datamodels/association/subject", "datamodels/association/subject_closure", "datamodels/association/subject_closure_label", "datamodels/association/subject_label", "datamodels/association/subjects_in_common", "datamodels/association/summary_group", "datamodels/association/supporting_objects", "datamodels/class-enrichment/Boolean", "datamodels/class-enrichment/ClassEnrichmentConfiguration", "datamodels/class-enrichment/ClassEnrichmentResult", "datamodels/class-enrichment/ClassEnrichmentResultSet", "datamodels/class-enrichment/Curie", "datamodels/class-enrichment/Date", "datamodels/class-enrichment/DateOrDatetime", "datamodels/class-enrichment/Datetime", "datamodels/class-enrichment/Decimal", "datamodels/class-enrichment/Double", "datamodels/class-enrichment/Float", "datamodels/class-enrichment/Integer", "datamodels/class-enrichment/Jsonpath", "datamodels/class-enrichment/Jsonpointer", "datamodels/class-enrichment/Ncname", "datamodels/class-enrichment/Nodeidentifier", "datamodels/class-enrichment/Objectidentifier", "datamodels/class-enrichment/Position", "datamodels/class-enrichment/SortFieldEnum", "datamodels/class-enrichment/Sparqlpath", "datamodels/class-enrichment/String", "datamodels/class-enrichment/Time", "datamodels/class-enrichment/Uri", "datamodels/class-enrichment/Uriorcurie", "datamodels/class-enrichment/ancestor_of_more_informative_result", "datamodels/class-enrichment/background_count", "datamodels/class-enrichment/background_total", "datamodels/class-enrichment/class-enrichment", "datamodels/class-enrichment/class_id", "datamodels/class-enrichment/class_label", "datamodels/class-enrichment/descendant_of_more_informative_result", "datamodels/class-enrichment/direction", "datamodels/class-enrichment/false_discovery_rate", "datamodels/class-enrichment/fold_enrichment", "datamodels/class-enrichment/index", "datamodels/class-enrichment/p_value", "datamodels/class-enrichment/p_value_adjusted", "datamodels/class-enrichment/p_value_cutoff", "datamodels/class-enrichment/probability", "datamodels/class-enrichment/rank", "datamodels/class-enrichment/results", "datamodels/class-enrichment/sample_count", "datamodels/class-enrichment/sample_total", "datamodels/cross-ontology-diff/Boolean", "datamodels/cross-ontology-diff/Curie", "datamodels/cross-ontology-diff/Date", "datamodels/cross-ontology-diff/DateOrDatetime", "datamodels/cross-ontology-diff/Datetime", "datamodels/cross-ontology-diff/Decimal", "datamodels/cross-ontology-diff/DiffCategory", "datamodels/cross-ontology-diff/Double", "datamodels/cross-ontology-diff/EntityReference", "datamodels/cross-ontology-diff/Float", "datamodels/cross-ontology-diff/Integer", "datamodels/cross-ontology-diff/Jsonpath", "datamodels/cross-ontology-diff/Jsonpointer", "datamodels/cross-ontology-diff/Label", "datamodels/cross-ontology-diff/MappingCardinalityEnum", "datamodels/cross-ontology-diff/Ncname", "datamodels/cross-ontology-diff/Nodeidentifier", "datamodels/cross-ontology-diff/Objectidentifier", "datamodels/cross-ontology-diff/Position", "datamodels/cross-ontology-diff/RelationalDiff", "datamodels/cross-ontology-diff/Source", "datamodels/cross-ontology-diff/Sparqlpath", "datamodels/cross-ontology-diff/String", "datamodels/cross-ontology-diff/StructureDiffResultSet", "datamodels/cross-ontology-diff/Time", "datamodels/cross-ontology-diff/Uri", "datamodels/cross-ontology-diff/Uriorcurie", "datamodels/cross-ontology-diff/category", "datamodels/cross-ontology-diff/cross-ontology-diff", "datamodels/cross-ontology-diff/index", "datamodels/cross-ontology-diff/is_functional", "datamodels/cross-ontology-diff/label", "datamodels/cross-ontology-diff/left_object_id", "datamodels/cross-ontology-diff/left_object_is_functional", "datamodels/cross-ontology-diff/left_object_label", "datamodels/cross-ontology-diff/left_object_name", "datamodels/cross-ontology-diff/left_predicate_id", "datamodels/cross-ontology-diff/left_predicate_label", "datamodels/cross-ontology-diff/left_predicate_name", "datamodels/cross-ontology-diff/left_side", "datamodels/cross-ontology-diff/left_source", "datamodels/cross-ontology-diff/left_subject_id", "datamodels/cross-ontology-diff/left_subject_is_functional", "datamodels/cross-ontology-diff/left_subject_label", "datamodels/cross-ontology-diff/left_subject_name", "datamodels/cross-ontology-diff/object", "datamodels/cross-ontology-diff/object_mapping_cardinality", "datamodels/cross-ontology-diff/object_mapping_predicate", "datamodels/cross-ontology-diff/predicate", "datamodels/cross-ontology-diff/results", "datamodels/cross-ontology-diff/right_intermediate_ids", "datamodels/cross-ontology-diff/right_object_id", "datamodels/cross-ontology-diff/right_object_label", "datamodels/cross-ontology-diff/right_object_name", "datamodels/cross-ontology-diff/right_predicate_ids", "datamodels/cross-ontology-diff/right_predicate_labels", "datamodels/cross-ontology-diff/right_predicate_names", "datamodels/cross-ontology-diff/right_side", "datamodels/cross-ontology-diff/right_source", "datamodels/cross-ontology-diff/right_subject_id", "datamodels/cross-ontology-diff/right_subject_label", "datamodels/cross-ontology-diff/right_subject_name", "datamodels/cross-ontology-diff/side", "datamodels/cross-ontology-diff/subject", "datamodels/cross-ontology-diff/subject_mapping_cardinality", "datamodels/cross-ontology-diff/subject_mapping_predicate", "datamodels/cross-ontology-diff/types", "datamodels/funowl/index", "datamodels/index", "datamodels/item-list/Boolean", "datamodels/item-list/Curie", "datamodels/item-list/Date", "datamodels/item-list/DateOrDatetime", "datamodels/item-list/Datetime", "datamodels/item-list/Decimal", "datamodels/item-list/Double", "datamodels/item-list/Float", "datamodels/item-list/Integer", "datamodels/item-list/ItemList", "datamodels/item-list/ItemListCollection", "datamodels/item-list/ItemListOrderType", "datamodels/item-list/Jsonpath", "datamodels/item-list/Jsonpointer", "datamodels/item-list/ListItem", "datamodels/item-list/Ncname", "datamodels/item-list/Nodeidentifier", "datamodels/item-list/Objectidentifier", "datamodels/item-list/Sparqlpath", "datamodels/item-list/String", "datamodels/item-list/Thing", "datamodels/item-list/Time", "datamodels/item-list/Uri", "datamodels/item-list/Uriorcurie", "datamodels/item-list/additionalType", "datamodels/item-list/categories", "datamodels/item-list/description", "datamodels/item-list/elementId", "datamodels/item-list/id", "datamodels/item-list/idType", "datamodels/item-list/identifiers", "datamodels/item-list/index", "datamodels/item-list/item", "datamodels/item-list/itemList", "datamodels/item-list/itemListElements", "datamodels/item-list/itemLists", "datamodels/item-list/itemMetadataMap", "datamodels/item-list/keywords", "datamodels/item-list/name", "datamodels/item-list/numberOfItems", "datamodels/item-list/position", "datamodels/item-list/previousItem", "datamodels/item-list/type", "datamodels/item-list/url", "datamodels/item-list/wasGeneratedBy", "datamodels/kgcl/index", "datamodels/lexical-index/Activity", "datamodels/lexical-index/Any", "datamodels/lexical-index/Boolean", "datamodels/lexical-index/Curie", "datamodels/lexical-index/Date", "datamodels/lexical-index/DateOrDatetime", "datamodels/lexical-index/Datetime", "datamodels/lexical-index/Decimal", "datamodels/lexical-index/Double", "datamodels/lexical-index/Float", "datamodels/lexical-index/Integer", "datamodels/lexical-index/Jsonpath", "datamodels/lexical-index/Jsonpointer", "datamodels/lexical-index/LexicalGrouping", "datamodels/lexical-index/LexicalIndex", "datamodels/lexical-index/LexicalTransformation", "datamodels/lexical-index/LexicalTransformationPipeline", "datamodels/lexical-index/Ncname", "datamodels/lexical-index/Nodeidentifier", "datamodels/lexical-index/Objectidentifier", "datamodels/lexical-index/RelationshipToTerm", "datamodels/lexical-index/Sparqlpath", "datamodels/lexical-index/String", "datamodels/lexical-index/Time", "datamodels/lexical-index/TransformationType", "datamodels/lexical-index/Uri", "datamodels/lexical-index/Uriorcurie", "datamodels/lexical-index/element", "datamodels/lexical-index/element_term", "datamodels/lexical-index/groupings", "datamodels/lexical-index/index", "datamodels/lexical-index/lexical-index", "datamodels/lexical-index/lexican-index", "datamodels/lexical-index/name", "datamodels/lexical-index/params", "datamodels/lexical-index/pipeline", "datamodels/lexical-index/pipelines", "datamodels/lexical-index/predicate", "datamodels/lexical-index/relationships", "datamodels/lexical-index/source", "datamodels/lexical-index/synonymized", "datamodels/lexical-index/term", "datamodels/lexical-index/transformations", "datamodels/lexical-index/type", "datamodels/lexical-index/types", "datamodels/mapping-rules/Activity", "datamodels/mapping-rules/Any", "datamodels/mapping-rules/Boolean", "datamodels/mapping-rules/Curie", "datamodels/mapping-rules/Date", "datamodels/mapping-rules/DateOrDatetime", "datamodels/mapping-rules/Datetime", "datamodels/mapping-rules/Decimal", "datamodels/mapping-rules/Double", "datamodels/mapping-rules/Float", "datamodels/mapping-rules/Integer", "datamodels/mapping-rules/Jsonpath", "datamodels/mapping-rules/Jsonpointer", "datamodels/mapping-rules/LexicalGrouping", "datamodels/mapping-rules/LexicalIndex", "datamodels/mapping-rules/LexicalTransformation", "datamodels/mapping-rules/LexicalTransformationPipeline", "datamodels/mapping-rules/MappingRule", "datamodels/mapping-rules/MappingRuleCollection", "datamodels/mapping-rules/Ncname", "datamodels/mapping-rules/Nodeidentifier", "datamodels/mapping-rules/Objectidentifier", "datamodels/mapping-rules/Postcondition", "datamodels/mapping-rules/Precondition", "datamodels/mapping-rules/RelationshipToTerm", "datamodels/mapping-rules/Sparqlpath", "datamodels/mapping-rules/String", "datamodels/mapping-rules/Synonymizer", "datamodels/mapping-rules/Test", "datamodels/mapping-rules/Time", "datamodels/mapping-rules/TransformationType", "datamodels/mapping-rules/Uri", "datamodels/mapping-rules/Uriorcurie", "datamodels/mapping-rules/description", "datamodels/mapping-rules/element", "datamodels/mapping-rules/element_term", "datamodels/mapping-rules/groupings", "datamodels/mapping-rules/index", "datamodels/mapping-rules/input", "datamodels/mapping-rules/lexical-index", "datamodels/mapping-rules/lexican-index", "datamodels/mapping-rules/mapping-rules", "datamodels/mapping-rules/mapping-rules-datamodel", "datamodels/mapping-rules/mapping_source_one_of", "datamodels/mapping-rules/match", "datamodels/mapping-rules/match_scope", "datamodels/mapping-rules/minimum_confidence", "datamodels/mapping-rules/name", "datamodels/mapping-rules/object_match_field_one_of", "datamodels/mapping-rules/object_source_one_of", "datamodels/mapping-rules/oneway", "datamodels/mapping-rules/output", "datamodels/mapping-rules/params", "datamodels/mapping-rules/pipeline", "datamodels/mapping-rules/pipelines", "datamodels/mapping-rules/postconditions", "datamodels/mapping-rules/preconditions", "datamodels/mapping-rules/predicate", "datamodels/mapping-rules/predicate_id", "datamodels/mapping-rules/predicate_id_one_of", "datamodels/mapping-rules/prefix", "datamodels/mapping-rules/qualifier", "datamodels/mapping-rules/relationships", "datamodels/mapping-rules/replacement", "datamodels/mapping-rules/rules", "datamodels/mapping-rules/source", "datamodels/mapping-rules/subject_match_field_one_of", "datamodels/mapping-rules/subject_source_one_of", "datamodels/mapping-rules/synonymized", "datamodels/mapping-rules/synonymizer", "datamodels/mapping-rules/term", "datamodels/mapping-rules/tests", "datamodels/mapping-rules/the_rule", "datamodels/mapping-rules/transformations", "datamodels/mapping-rules/transformations_included_in", "datamodels/mapping-rules/type", "datamodels/mapping-rules/types", "datamodels/mapping-rules/weight", "datamodels/obograph/Axiom", "datamodels/obograph/BasicPropertyValue", "datamodels/obograph/Boolean", "datamodels/obograph/Curie", "datamodels/obograph/Date", "datamodels/obograph/DateOrDatetime", "datamodels/obograph/Datetime", "datamodels/obograph/Decimal", "datamodels/obograph/DefinitionPropertyValue", "datamodels/obograph/DisjointClassExpressionsAxiom", "datamodels/obograph/DomainRangeAxiom", "datamodels/obograph/Double", "datamodels/obograph/Edge", "datamodels/obograph/EquivalentNodesSet", "datamodels/obograph/ExistentialRestrictionExpression", "datamodels/obograph/Float", "datamodels/obograph/Graph", "datamodels/obograph/GraphDocument", "datamodels/obograph/Integer", "datamodels/obograph/Jsonpath", "datamodels/obograph/Jsonpointer", "datamodels/obograph/LogicalDefinitionAxiom", "datamodels/obograph/Meta", "datamodels/obograph/Ncname", "datamodels/obograph/Node", "datamodels/obograph/NodeTypeEnum", "datamodels/obograph/Nodeidentifier", "datamodels/obograph/Objectidentifier", "datamodels/obograph/OboIdentifierString", "datamodels/obograph/PredsEnum", "datamodels/obograph/PrefixDeclaration", "datamodels/obograph/PropertyChainAxiom", "datamodels/obograph/PropertyTypeEnum", "datamodels/obograph/PropertyValue", "datamodels/obograph/ScopeEnum", "datamodels/obograph/ScopesEnum", "datamodels/obograph/Sparqlpath", "datamodels/obograph/String", "datamodels/obograph/SubsetDefinition", "datamodels/obograph/SynonymPropertyValue", "datamodels/obograph/SynonymTypeDefinition", "datamodels/obograph/SynonymTypeIdentifierString", "datamodels/obograph/Time", "datamodels/obograph/Uri", "datamodels/obograph/Uriorcurie", "datamodels/obograph/XrefPropertyValue", "datamodels/obograph/XrefString", "datamodels/obograph/allValuesFromEdges", "datamodels/obograph/basicPropertyValues", "datamodels/obograph/chainPredicateIds", "datamodels/obograph/classExpressions", "datamodels/obograph/classIds", "datamodels/obograph/comments", "datamodels/obograph/definedClassId", "datamodels/obograph/definition", "datamodels/obograph/deprecated", "datamodels/obograph/disjointClassExpressionsAxioms", "datamodels/obograph/domainClassIds", "datamodels/obograph/domainRangeAxioms", "datamodels/obograph/edges", "datamodels/obograph/equivalentNodesSets", "datamodels/obograph/fillerId", "datamodels/obograph/genusIds", "datamodels/obograph/graphs", "datamodels/obograph/id", "datamodels/obograph/index", "datamodels/obograph/isExact", "datamodels/obograph/label", "datamodels/obograph/lang", "datamodels/obograph/lbl", "datamodels/obograph/logicalDefinitionAxioms", "datamodels/obograph/meta", "datamodels/obograph/namespace", "datamodels/obograph/nodeIds", "datamodels/obograph/nodes", "datamodels/obograph/obj", "datamodels/obograph/obographs_datamodel", "datamodels/obograph/obographs_linkml_model", "datamodels/obograph/pred", "datamodels/obograph/predicateId", "datamodels/obograph/prefix", "datamodels/obograph/prefixes", "datamodels/obograph/propertyChainAxioms", "datamodels/obograph/propertyId", "datamodels/obograph/propertyType", "datamodels/obograph/rangeClassIds", "datamodels/obograph/representativeNodeId", "datamodels/obograph/representitiveNodeId", "datamodels/obograph/restrictions", "datamodels/obograph/scope", "datamodels/obograph/sub", "datamodels/obograph/subsetDefinitions", "datamodels/obograph/subsets", "datamodels/obograph/synonymType", "datamodels/obograph/synonymTypeDefinitions", "datamodels/obograph/synonyms", "datamodels/obograph/type", "datamodels/obograph/types", "datamodels/obograph/unionEquivalentTo", "datamodels/obograph/unionEquivalentToExpression", "datamodels/obograph/val", "datamodels/obograph/valType", "datamodels/obograph/version", "datamodels/obograph/xrefs", "datamodels/ontology-metadata/Agent", "datamodels/ontology-metadata/AllotropePermittedProfile", "datamodels/ontology-metadata/AllotropeRequiredProfile", "datamodels/ontology-metadata/Annotation", "datamodels/ontology-metadata/AnnotationProperty", "datamodels/ontology-metadata/AnnotationPropertyMixin", "datamodels/ontology-metadata/Anonymous", "datamodels/ontology-metadata/AnonymousClassExpression", "datamodels/ontology-metadata/Any", "datamodels/ontology-metadata/Axiom", "datamodels/ontology-metadata/Boolean", "datamodels/ontology-metadata/CURIELiteral", "datamodels/ontology-metadata/Class", "datamodels/ontology-metadata/ClassExpression", "datamodels/ontology-metadata/Curie", "datamodels/ontology-metadata/Date", "datamodels/ontology-metadata/DateOrDatetime", "datamodels/ontology-metadata/Datetime", "datamodels/ontology-metadata/Decimal", "datamodels/ontology-metadata/DefinitionConstraintComponent", "datamodels/ontology-metadata/Double", "datamodels/ontology-metadata/Expression", "datamodels/ontology-metadata/Float", "datamodels/ontology-metadata/GoPermittedProfile", "datamodels/ontology-metadata/GoRecommendedProfile", "datamodels/ontology-metadata/GoRequiredProfile", "datamodels/ontology-metadata/HasCategory", "datamodels/ontology-metadata/HasLifeCycle", "datamodels/ontology-metadata/HasMappings", "datamodels/ontology-metadata/HasMinimalMetadata", "datamodels/ontology-metadata/HasProvenance", "datamodels/ontology-metadata/HasSynonyms", "datamodels/ontology-metadata/HasUserInformation", "datamodels/ontology-metadata/HomoSapiens", "datamodels/ontology-metadata/IEDB_alternative_term", "datamodels/ontology-metadata/ISA_alternative_term", "datamodels/ontology-metadata/Image", "datamodels/ontology-metadata/Integer", "datamodels/ontology-metadata/IriType", "datamodels/ontology-metadata/Jsonpath", "datamodels/ontology-metadata/Jsonpointer", "datamodels/ontology-metadata/LabelType", "datamodels/ontology-metadata/NCIT_definition_source", "datamodels/ontology-metadata/NCIT_term_source", "datamodels/ontology-metadata/NCIT_term_type", "datamodels/ontology-metadata/NamedIndividual", "datamodels/ontology-metadata/NamedObject", "datamodels/ontology-metadata/NarrativeText", "datamodels/ontology-metadata/Ncname", "datamodels/ontology-metadata/Nodeidentifier", "datamodels/ontology-metadata/NotObsoleteAspect", "datamodels/ontology-metadata/OBO_foundry_unique_label", "datamodels/ontology-metadata/ObiPermittedProfile", "datamodels/ontology-metadata/ObiRequiredProfile", "datamodels/ontology-metadata/ObjectProperty", "datamodels/ontology-metadata/Objectidentifier", "datamodels/ontology-metadata/ObsoleteAspect", "datamodels/ontology-metadata/Ontology", "datamodels/ontology-metadata/Ontology-Metadata", "datamodels/ontology-metadata/Property", "datamodels/ontology-metadata/PropertyExpression", "datamodels/ontology-metadata/Restriction", "datamodels/ontology-metadata/Sparqlpath", "datamodels/ontology-metadata/String", "datamodels/ontology-metadata/Subset", "datamodels/ontology-metadata/Term", "datamodels/ontology-metadata/Thing", "datamodels/ontology-metadata/TidyString", "datamodels/ontology-metadata/Time", "datamodels/ontology-metadata/TransitiveProperty", "datamodels/ontology-metadata/URLLiteral", "datamodels/ontology-metadata/Uri", "datamodels/ontology-metadata/Uriorcurie", "datamodels/ontology-metadata/allValuesFrom", "datamodels/ontology-metadata/alternative_term", "datamodels/ontology-metadata/annotatedProperty", "datamodels/ontology-metadata/annotatedSource", "datamodels/ontology-metadata/annotatedTarget", "datamodels/ontology-metadata/annotations", "datamodels/ontology-metadata/broadMatch", "datamodels/ontology-metadata/cardinality", "datamodels/ontology-metadata/category", "datamodels/ontology-metadata/changeNote", "datamodels/ontology-metadata/closeMatch", "datamodels/ontology-metadata/comment", "datamodels/ontology-metadata/complementOf", "datamodels/ontology-metadata/conformsTo", "datamodels/ontology-metadata/consider", "datamodels/ontology-metadata/contributor", "datamodels/ontology-metadata/core_property", "datamodels/ontology-metadata/created", "datamodels/ontology-metadata/created_by", "datamodels/ontology-metadata/creation_date", "datamodels/ontology-metadata/creator", "datamodels/ontology-metadata/curator_note", "datamodels/ontology-metadata/database_cross_reference", "datamodels/ontology-metadata/date", "datamodels/ontology-metadata/date_retrieved", "datamodels/ontology-metadata/defaultLanguage", "datamodels/ontology-metadata/definition", "datamodels/ontology-metadata/definition_source", "datamodels/ontology-metadata/depicted_by", "datamodels/ontology-metadata/deprecated", "datamodels/ontology-metadata/disconnected_from", "datamodels/ontology-metadata/disjointWith", "datamodels/ontology-metadata/distinctMembers", "datamodels/ontology-metadata/domain", "datamodels/ontology-metadata/editor_note", "datamodels/ontology-metadata/editor_preferred_term", "datamodels/ontology-metadata/equivalentClass", "datamodels/ontology-metadata/equivalentProperty", "datamodels/ontology-metadata/evidence", "datamodels/ontology-metadata/exactMatch", "datamodels/ontology-metadata/example_of_usage", "datamodels/ontology-metadata/excluded_axiom", "datamodels/ontology-metadata/excluded_from_QC_check", "datamodels/ontology-metadata/excluded_subClassOf", "datamodels/ontology-metadata/excluded_synonym", "datamodels/ontology-metadata/external_ontology", "datamodels/ontology-metadata/hasValue", "datamodels/ontology-metadata/has_alternative_id", "datamodels/ontology-metadata/has_axiom_label", "datamodels/ontology-metadata/has_broad_synonym", "datamodels/ontology-metadata/has_curation_status", "datamodels/ontology-metadata/has_exact_synonym", "datamodels/ontology-metadata/has_narrow_synonym", "datamodels/ontology-metadata/has_obo_namespace", "datamodels/ontology-metadata/has_obsolescence_reason", "datamodels/ontology-metadata/has_ontology_root_term", "datamodels/ontology-metadata/has_rank", "datamodels/ontology-metadata/has_related_synonym", "datamodels/ontology-metadata/has_synonym_type", "datamodels/ontology-metadata/id", "datamodels/ontology-metadata/image", "datamodels/ontology-metadata/imported_from", "datamodels/ontology-metadata/imports", "datamodels/ontology-metadata/in_subset", "datamodels/ontology-metadata/index", "datamodels/ontology-metadata/informative_property", "datamodels/ontology-metadata/intersectionOf", "datamodels/ontology-metadata/inverseOf", "datamodels/ontology-metadata/isDefinedBy", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive", "datamodels/ontology-metadata/is_class_level", "datamodels/ontology-metadata/is_cyclic", "datamodels/ontology-metadata/is_inferred", "datamodels/ontology-metadata/is_metadata_tag", "datamodels/ontology-metadata/is_transitive", "datamodels/ontology-metadata/label", "datamodels/ontology-metadata/language", "datamodels/ontology-metadata/license", "datamodels/ontology-metadata/logical_predicate", "datamodels/ontology-metadata/match", "datamodels/ontology-metadata/match_aspect", "datamodels/ontology-metadata/maxQualifiedCardinality", "datamodels/ontology-metadata/members", "datamodels/ontology-metadata/minCardinality", "datamodels/ontology-metadata/minQualifiedCardinality", "datamodels/ontology-metadata/narrowMatch", "datamodels/ontology-metadata/never_in_taxon", "datamodels/ontology-metadata/notes", "datamodels/ontology-metadata/object", "datamodels/ontology-metadata/oboInOwl_id", "datamodels/ontology-metadata/oboInOwl_ontology", "datamodels/ontology-metadata/obsoletion_related_property", "datamodels/ontology-metadata/omo-schema", "datamodels/ontology-metadata/onClass", "datamodels/ontology-metadata/onProperty", "datamodels/ontology-metadata/oneOf", "datamodels/ontology-metadata/ontology_term_requester", "datamodels/ontology-metadata/page", "datamodels/ontology-metadata/predicate", "datamodels/ontology-metadata/propertyChainAxiom", "datamodels/ontology-metadata/provenance_property", "datamodels/ontology-metadata/qualifiedCardinality", "datamodels/ontology-metadata/range", "datamodels/ontology-metadata/reification_predicate", "datamodels/ontology-metadata/sameAs", "datamodels/ontology-metadata/seeAlso", "datamodels/ontology-metadata/shortcut_annotation_property", "datamodels/ontology-metadata/shorthand", "datamodels/ontology-metadata/should_conform_to", "datamodels/ontology-metadata/someValuesFrom", "datamodels/ontology-metadata/source", "datamodels/ontology-metadata/subClassOf", "datamodels/ontology-metadata/synonym", "datamodels/ontology-metadata/temporal_interpretation", "datamodels/ontology-metadata/term_editor", "datamodels/ontology-metadata/term_replaced_by", "datamodels/ontology-metadata/term_tracker_item", "datamodels/ontology-metadata/title", "datamodels/ontology-metadata/type", "datamodels/ontology-metadata/types", "datamodels/ontology-metadata/unionOf", "datamodels/ontology-metadata/url", "datamodels/ontology-metadata/versionIRI", "datamodels/ontology-metadata/versionInfo", "datamodels/ontology-metadata/version_property", "datamodels/search/Boolean", "datamodels/search/BooleanOperator", "datamodels/search/ComplexQuery", "datamodels/search/Curie", "datamodels/search/Date", "datamodels/search/DateOrDatetime", "datamodels/search/Datetime", "datamodels/search/Decimal", "datamodels/search/Double", "datamodels/search/Float", "datamodels/search/GraphFunction", "datamodels/search/Integer", "datamodels/search/Jsonpath", "datamodels/search/Jsonpointer", "datamodels/search/Ncname", "datamodels/search/Nodeidentifier", "datamodels/search/Objectidentifier", "datamodels/search/PathExpression", "datamodels/search/SearchBaseConfiguration", "datamodels/search/SearchProperty", "datamodels/search/SearchResult", "datamodels/search/SearchResultSet", "datamodels/search/SearchTerm", "datamodels/search/SearchTermSyntax", "datamodels/search/Sparqlpath", "datamodels/search/String", "datamodels/search/Time", "datamodels/search/Uri", "datamodels/search/Uriorcurie", "datamodels/search/all_of", "datamodels/search/any_of", "datamodels/search/atom", "datamodels/search/categories", "datamodels/search/configuration", "datamodels/search/cursor", "datamodels/search/force_case_insensitive", "datamodels/search/graph_predicates", "datamodels/search/include_aliases", "datamodels/search/include_definition", "datamodels/search/include_id", "datamodels/search/include_label", "datamodels/search/include_obsoletes_in_results", "datamodels/search/index", "datamodels/search/is_complete", "datamodels/search/is_fuzzy", "datamodels/search/is_partial", "datamodels/search/is_regular_expression", "datamodels/search/limit", "datamodels/search/matches_full_search_term", "datamodels/search/none_of", "datamodels/search/object_id", "datamodels/search/object_label", "datamodels/search/object_match_field", "datamodels/search/object_source", "datamodels/search/object_source_version", "datamodels/search/path_to", "datamodels/search/properties", "datamodels/search/rank", "datamodels/search/result_count", "datamodels/search/results", "datamodels/search/search-datamodel", "datamodels/search/search_term", "datamodels/search/search_terms", "datamodels/search/snippet", "datamodels/search/syntax", "datamodels/search/traversal", "datamodels/search/types", "datamodels/semsql/index", "datamodels/similarity/BestMatch", "datamodels/similarity/Boolean", "datamodels/similarity/Curie", "datamodels/similarity/Date", "datamodels/similarity/DateOrDatetime", "datamodels/similarity/Datetime", "datamodels/similarity/Decimal", "datamodels/similarity/Double", "datamodels/similarity/Float", "datamodels/similarity/Integer", "datamodels/similarity/ItemCount", "datamodels/similarity/Jsonpath", "datamodels/similarity/Jsonpointer", "datamodels/similarity/Ncname", "datamodels/similarity/NegativeLogValue", "datamodels/similarity/Nodeidentifier", "datamodels/similarity/NonNegativeFloat", "datamodels/similarity/Objectidentifier", "datamodels/similarity/PairwiseSimilarity", "datamodels/similarity/Sparqlpath", "datamodels/similarity/String", "datamodels/similarity/TermInfo", "datamodels/similarity/TermPairwiseSimilarity", "datamodels/similarity/TermSetPairwiseSimilarity", "datamodels/similarity/Time", "datamodels/similarity/Uri", "datamodels/similarity/Uriorcurie", "datamodels/similarity/ZeroToOne", "datamodels/similarity/ancestor_id", "datamodels/similarity/ancestor_information_content", "datamodels/similarity/ancestor_label", "datamodels/similarity/ancestor_source", "datamodels/similarity/average_score", "datamodels/similarity/best_score", "datamodels/similarity/cosine_similarity", "datamodels/similarity/dice_similarity", "datamodels/similarity/id", "datamodels/similarity/index", "datamodels/similarity/information_content", "datamodels/similarity/intersection_count", "datamodels/similarity/jaccard_similarity", "datamodels/similarity/label", "datamodels/similarity/match_source", "datamodels/similarity/match_source_label", "datamodels/similarity/match_subsumer", "datamodels/similarity/match_subsumer_label", "datamodels/similarity/match_target", "datamodels/similarity/match_target_label", "datamodels/similarity/metric", "datamodels/similarity/object_best_matches", "datamodels/similarity/object_id", "datamodels/similarity/object_information_content", "datamodels/similarity/object_label", "datamodels/similarity/object_source", "datamodels/similarity/object_termset", "datamodels/similarity/overlap_coefficient", "datamodels/similarity/phenodigm_score", "datamodels/similarity/score", "datamodels/similarity/similarity", "datamodels/similarity/subject_best_matches", "datamodels/similarity/subject_id", "datamodels/similarity/subject_information_content", "datamodels/similarity/subject_label", "datamodels/similarity/subject_source", "datamodels/similarity/subject_termset", "datamodels/similarity/subsumed_by_score", "datamodels/similarity/subsumes_score", "datamodels/similarity/types", "datamodels/similarity/union_count", "datamodels/sssom/index", "datamodels/summary-statistics/Agent", "datamodels/summary-statistics/Boolean", "datamodels/summary-statistics/ChangeTypeStatistic", "datamodels/summary-statistics/ContributorRole", "datamodels/summary-statistics/ContributorStatistics", "datamodels/summary-statistics/Curie", "datamodels/summary-statistics/Date", "datamodels/summary-statistics/DateOrDatetime", "datamodels/summary-statistics/Datetime", "datamodels/summary-statistics/Decimal", "datamodels/summary-statistics/Double", "datamodels/summary-statistics/FacetStatistics", "datamodels/summary-statistics/FacetedCount", "datamodels/summary-statistics/Float", "datamodels/summary-statistics/GlobalStatistics", "datamodels/summary-statistics/GroupedStatistics", "datamodels/summary-statistics/Integer", "datamodels/summary-statistics/Jsonpath", "datamodels/summary-statistics/Jsonpointer", "datamodels/summary-statistics/Ncname", "datamodels/summary-statistics/Nodeidentifier", "datamodels/summary-statistics/Objectidentifier", "datamodels/summary-statistics/Ontology", "datamodels/summary-statistics/Sparqlpath", "datamodels/summary-statistics/String", "datamodels/summary-statistics/SummaryStatisticCollection", "datamodels/summary-statistics/SummaryStatisticsCalculationActivity", "datamodels/summary-statistics/SummaryStatisticsReport", "datamodels/summary-statistics/Time", "datamodels/summary-statistics/UngroupedStatistics", "datamodels/summary-statistics/Uri", "datamodels/summary-statistics/Uriorcurie", "datamodels/summary-statistics/acted_on_behalf_of", "datamodels/summary-statistics/agents", "datamodels/summary-statistics/annotation_property_count", "datamodels/summary-statistics/anonymous_class_expression_count", "datamodels/summary-statistics/anonymous_individual_count", "datamodels/summary-statistics/by_category", "datamodels/summary-statistics/by_ontology", "datamodels/summary-statistics/by_subset", "datamodels/summary-statistics/by_taxon", "datamodels/summary-statistics/change_summary", "datamodels/summary-statistics/class_count", "datamodels/summary-statistics/class_count_by_category", "datamodels/summary-statistics/class_count_by_subset", "datamodels/summary-statistics/class_count_excluding_deprecated", "datamodels/summary-statistics/class_count_with_definitions", "datamodels/summary-statistics/class_count_with_text_definitions", "datamodels/summary-statistics/class_count_without_text_definitions", "datamodels/summary-statistics/class_statistic_group", "datamodels/summary-statistics/compared_with", "datamodels/summary-statistics/contributor_id", "datamodels/summary-statistics/contributor_name", "datamodels/summary-statistics/contributor_summary", "datamodels/summary-statistics/count_statistic", "datamodels/summary-statistics/datatype_property_count", "datamodels/summary-statistics/deprecated_class_count", "datamodels/summary-statistics/deprecated_object_property_count", "datamodels/summary-statistics/description", "datamodels/summary-statistics/description_logic_profile", "datamodels/summary-statistics/distinct_synonym_count", "datamodels/summary-statistics/edge_count_by_predicate", "datamodels/summary-statistics/ended_at_time", "datamodels/summary-statistics/entailed_edge_count_by_predicate", "datamodels/summary-statistics/equivalent_classes_axiom_count", "datamodels/summary-statistics/equivalentclasses_axiom_count", "datamodels/summary-statistics/facet", "datamodels/summary-statistics/filtered_count", "datamodels/summary-statistics/id", "datamodels/summary-statistics/index", "datamodels/summary-statistics/individual_count", "datamodels/summary-statistics/individual_statistic_group", "datamodels/summary-statistics/label", "datamodels/summary-statistics/mapping_count", "datamodels/summary-statistics/mapping_statement_count_by_object_source", "datamodels/summary-statistics/mapping_statement_count_by_predicate", "datamodels/summary-statistics/mapping_statement_count_subject_by_object_source", "datamodels/summary-statistics/merged_class_count", "datamodels/summary-statistics/metadata_statistic_group", "datamodels/summary-statistics/named_individual_count", "datamodels/summary-statistics/non_deprecated_class_count", "datamodels/summary-statistics/non_deprecated_object_property_count", "datamodels/summary-statistics/normalization_comments", "datamodels/summary-statistics/object_property_count", "datamodels/summary-statistics/ontologies", "datamodels/summary-statistics/ontology_count", "datamodels/summary-statistics/owl_axiom_count", "datamodels/summary-statistics/owl_statistic_group", "datamodels/summary-statistics/partitions", "datamodels/summary-statistics/prefix", "datamodels/summary-statistics/property_count", "datamodels/summary-statistics/property_statistic_group", "datamodels/summary-statistics/rdf_triple_count", "datamodels/summary-statistics/role_counts", "datamodels/summary-statistics/started_at_time", "datamodels/summary-statistics/subclass_of_axiom_count", "datamodels/summary-statistics/subset_count", "datamodels/summary-statistics/summary-statistics", "datamodels/summary-statistics/synonym_statement_count", "datamodels/summary-statistics/synonym_statement_count_by_predicate", "datamodels/summary-statistics/title", "datamodels/summary-statistics/types", "datamodels/summary-statistics/unsatisfiable_class_count", "datamodels/summary-statistics/untyped_entity_count", "datamodels/summary-statistics/version", "datamodels/summary-statistics/version_info", "datamodels/summary-statistics/was_associated_with", "datamodels/summary-statistics/was_generated_by", "datamodels/taxon-constraints/Boolean", "datamodels/taxon-constraints/ConfigurationOption", "datamodels/taxon-constraints/Curie", "datamodels/taxon-constraints/Date", "datamodels/taxon-constraints/DateOrDatetime", "datamodels/taxon-constraints/Datetime", "datamodels/taxon-constraints/Decimal", "datamodels/taxon-constraints/Double", "datamodels/taxon-constraints/Float", "datamodels/taxon-constraints/Integer", "datamodels/taxon-constraints/Jsonpath", "datamodels/taxon-constraints/Jsonpointer", "datamodels/taxon-constraints/Ncname", "datamodels/taxon-constraints/Nodeidentifier", "datamodels/taxon-constraints/Objectidentifier", "datamodels/taxon-constraints/PredicateTerm", "datamodels/taxon-constraints/Sparqlpath", "datamodels/taxon-constraints/String", "datamodels/taxon-constraints/SubjectTerm", "datamodels/taxon-constraints/Taxon", "datamodels/taxon-constraints/TaxonConstraint", "datamodels/taxon-constraints/Term", "datamodels/taxon-constraints/Time", "datamodels/taxon-constraints/Uri", "datamodels/taxon-constraints/Uriorcurie", "datamodels/taxon-constraints/asserted", "datamodels/taxon-constraints/candidate", "datamodels/taxon-constraints/comments", "datamodels/taxon-constraints/contradicted_by", "datamodels/taxon-constraints/description", "datamodels/taxon-constraints/evolutionary", "datamodels/taxon-constraints/id", "datamodels/taxon-constraints/index", "datamodels/taxon-constraints/label", "datamodels/taxon-constraints/never_in", "datamodels/taxon-constraints/only_in", "datamodels/taxon-constraints/predicate", "datamodels/taxon-constraints/predicates", "datamodels/taxon-constraints/present_in", "datamodels/taxon-constraints/present_in_ancestor_of", "datamodels/taxon-constraints/redundant", "datamodels/taxon-constraints/redundant_with", "datamodels/taxon-constraints/redundant_with_only_in", "datamodels/taxon-constraints/sources", "datamodels/taxon-constraints/subject", "datamodels/taxon-constraints/taxon", "datamodels/taxon-constraints/taxon-constraints", "datamodels/taxon-constraints/unsatisfiable", "datamodels/taxon-constraints/via_terms", "datamodels/text-annotator/Boolean", "datamodels/text-annotator/Curie", "datamodels/text-annotator/Date", "datamodels/text-annotator/DateOrDatetime", "datamodels/text-annotator/Datetime", "datamodels/text-annotator/Decimal", "datamodels/text-annotator/Double", "datamodels/text-annotator/Float", "datamodels/text-annotator/HasSpan", "datamodels/text-annotator/Integer", "datamodels/text-annotator/Jsonpath", "datamodels/text-annotator/Jsonpointer", "datamodels/text-annotator/Ncname", "datamodels/text-annotator/Nodeidentifier", "datamodels/text-annotator/Objectidentifier", "datamodels/text-annotator/Position", "datamodels/text-annotator/Sparqlpath", "datamodels/text-annotator/String", "datamodels/text-annotator/TextAnnotation", "datamodels/text-annotator/TextAnnotationConfiguration", "datamodels/text-annotator/TextAnnotationResultSet", "datamodels/text-annotator/TextualElement", "datamodels/text-annotator/Time", "datamodels/text-annotator/TransformationType", "datamodels/text-annotator/Uri", "datamodels/text-annotator/Uriorcurie", "datamodels/text-annotator/annotations", "datamodels/text-annotator/categories", "datamodels/text-annotator/confidence", "datamodels/text-annotator/id", "datamodels/text-annotator/include_aliases", "datamodels/text-annotator/index", "datamodels/text-annotator/info", "datamodels/text-annotator/is_longest_match", "datamodels/text-annotator/limit", 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393, 431, 437, 446, 460, 470, 471, 1102, 1117, 1119, 1137, 1145, 1166, 1172, 1173, 1180, 1192], "includ": [0, 1, 2, 21, 45, 46, 388, 431, 437, 446, 448, 502, 503, 504, 505, 506, 507, 508, 510, 511, 527, 541, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 625, 635, 646, 647, 655, 658, 664, 665, 666, 668, 694, 717, 735, 842, 876, 882, 886, 898, 989, 997, 1000, 1001, 1046, 1067, 1097, 1100, 1101, 1106, 1108, 1109, 1110, 1113, 1114, 1115, 1117, 1118, 1119, 1123, 1126, 1129, 1131, 1136, 1137, 1141, 1145, 1165, 1166, 1167, 1168, 1169, 1171, 1172, 1175, 1176, 1178, 1179, 1180, 1181, 1192], "proven": [0, 212, 234, 247, 405, 437, 1108], "In": [0, 1, 2, 212, 227, 942, 953, 1099, 1106, 1107, 1108, 1109, 1110, 1111, 1113, 1115, 1116, 1117, 1118, 1119, 1126, 1129, 1131, 1132, 1135, 1140, 1145, 1158, 1159, 1166, 1173, 1182, 1192], "futur": [0, 1102, 1105, 1106, 1113, 1118, 1123, 1129, 1130, 1135, 1136, 1140, 1159, 1165, 1172, 1173, 1178, 1182], "mai": [0, 1, 2, 4, 6, 21, 45, 49, 51, 95, 135, 202, 204, 212, 227, 252, 297, 335, 375, 382, 418, 490, 678, 745, 818, 825, 827, 828, 901, 923, 939, 940, 941, 952, 953, 954, 959, 966, 971, 1029, 1102, 1105, 1106, 1107, 1108, 1109, 1113, 1114, 1115, 1116, 1117, 1118, 1123, 1126, 1129, 1135, 1136, 1140, 1141, 1149, 1158, 1159, 1166, 1167, 1170, 1172, 1173, 1174, 1176, 1178, 1179, 1180, 1181, 1182, 1191, 1192], "becom": [0, 4, 42, 46, 49, 51, 316, 352, 1115, 1118, 1145], "true": [0, 3, 4, 5, 17, 20, 21, 22, 24, 32, 33, 36, 37, 38, 41, 42, 45, 46, 49, 50, 51, 53, 61, 63, 65, 66, 70, 77, 79, 80, 81, 82, 83, 85, 86, 88, 90, 91, 92, 93, 94, 119, 125, 126, 128, 131, 134, 153, 157, 163, 164, 165, 166, 167, 170, 173, 175, 176, 179, 182, 183, 184, 188, 189, 191, 196, 197, 203, 212, 213, 217, 223, 227, 228, 230, 233, 234, 235, 237, 238, 239, 240, 247, 249, 251, 262, 263, 264, 265, 269, 278, 279, 282, 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1111, 1115, 1118, 1124, 1126, 1127, 1128, 1129, 1132, 1136, 1141, 1182, 1184, 1191, 1192], "api": [0, 1102, 1103, 1106, 1118, 1123, 1124, 1129, 1136, 1137, 1140, 1148, 1150, 1151, 1152, 1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1165, 1166, 1167, 1168, 1169, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 1180, 1181, 1183], "incatool": [0, 495, 1100, 1106, 1124, 1163, 1192], "github": [0, 2, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 470, 471, 472, 473, 474, 475, 476, 480, 488, 495, 503, 509, 512, 521, 530, 535, 540, 541, 545, 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1100, 1107, 1108, 1115, 1118, 1119, 1136, 1137, 1141, 1165], "shorthand": [0, 480, 530, 540, 545, 613, 1106, 1108, 1182], "m": [0, 1114, 1123, 1129, 1151, 1166], "method": [0, 1, 1099, 1102, 1103, 1106, 1107, 1113, 1115, 1117, 1118, 1119, 1130, 1131, 1132, 1136, 1141, 1156, 1159, 1165, 1166, 1170, 1171, 1172, 1178, 1180, 1181, 1182, 1192], "graph_traversal_method": 0, "whether": [0, 1106, 1107, 1115, 1116, 1119, 1137, 1141, 1145, 1161, 1166, 1167, 1168, 1169, 1170, 1171, 1175, 1176, 1178, 1181], "formal": [0, 1, 381, 437, 939, 955, 956, 1100, 1106, 1108, 1109, 1110, 1117, 1123, 1166, 1178], "entail": [0, 140, 153, 163, 842, 876, 882, 1100, 1106, 1111, 1113, 1131, 1166, 1173, 1178, 1179], "walk": [0, 1106, 1117, 1130, 1133, 1172], "hop": [0, 1106, 1117], "each": [0, 1, 140, 153, 161, 163, 202, 273, 321, 324, 331, 365, 437, 448, 827, 993, 1100, 1102, 1106, 1107, 1109, 1117, 1118, 1119, 1123, 1126, 1129, 1132, 1140, 1141, 1145, 1163, 1166, 1168, 1169, 1171, 1175, 1176, 1178, 1180, 1181, 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"docstr": [2, 1102], "read": [2, 1104, 1109, 1111, 1136], "architectur": [2, 1103, 1127, 1129, 1164], "best": [2, 1105, 1118, 1123, 1165, 1182], "practic": [2, 1105, 1107, 1113, 1115, 1116, 1118, 1166, 1192], "sooner": 2, "mark": [2, 1115, 1117], "draft": 2, "readi": [2, 1124, 1128], "review": [2, 1113, 1123], "sure": [2, 1126, 1129], "unit": [2, 263, 278, 279, 285, 308, 321, 330, 331, 348, 365, 1102], "print": [2, 1099, 1107, 1110, 1114, 1115, 1116, 1117, 1126, 1130, 1131, 1137, 1140, 1141, 1145, 1148, 1154, 1156, 1158, 1159, 1165, 1166, 1167, 1170, 1171, 1172, 1176, 1180, 1192], "ing": 2, "log": [2, 780, 781, 1118], "diagnost": [2, 1118], "captur": [2, 372, 437, 443, 1108, 1166], "exemplar": 2, "regist": [2, 418], "scheme": [2, 1126, 1154, 1160, 1162, 1164], "__init__": [2, 1156, 1157, 1161, 1163], "py": [2, 812, 1130, 1150, 1156, 1157, 1159, 1160, 1161, 1162, 1163, 1173], "__post_init__": [2, 1126], "cli": [2, 1102, 1120, 1123, 1129, 1141, 1182, 1192], "refactor": 2, "substanti": 2, "ad": [2, 212, 227, 234, 1107, 1112, 1113, 1117, 1123, 1126, 1136, 1137, 1138], "diff": [2, 4, 42, 46, 56, 71, 89, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 158, 159, 160, 161, 164, 165, 166, 167, 168, 170, 171, 173, 174, 175, 176, 177, 179, 180, 181, 182, 183, 184, 185, 186, 188, 189, 191, 192, 193, 194, 196, 197, 198, 199, 202, 815, 828, 840, 842, 863, 879, 880, 882, 1106, 1127, 1168, 1170, 1174], "coordin": 2, "advanc": [2, 1102, 1106, 1107, 1112, 1117, 1128, 1135, 1151, 1166, 1180], "dev": [2, 1135], "environ": [2, 1109, 1123, 1129], "test_implement": 2, "test_util": 2, "author": 2, "makefil": 2, "set": [2, 3, 4, 17, 21, 22, 30, 36, 42, 45, 46, 65, 66, 77, 78, 80, 81, 85, 86, 118, 125, 213, 234, 238, 381, 388, 389, 393, 422, 423, 425, 432, 434, 435, 437, 443, 453, 460, 470, 471, 766, 775, 776, 780, 791, 792, 797, 802, 807, 842, 857, 882, 909, 941, 949, 953, 957, 961, 962, 1055, 1058, 1067, 1070, 1084, 1093, 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1180, 1181, 1192, 1193], "oa": [3, 4, 17, 22, 23, 60, 84, 978, 988, 1020, 1165], "annot": [3, 31, 46, 202, 372, 373, 380, 381, 382, 384, 385, 388, 389, 394, 396, 403, 404, 405, 411, 417, 420, 424, 426, 427, 437, 443, 446, 464, 467, 474, 475, 481, 485, 507, 613, 638, 648, 824, 827, 838, 842, 882, 978, 988, 989, 990, 998, 1000, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1015, 1018, 1019, 1020, 1021, 1022, 1025, 1061, 1099, 1103, 1106, 1107, 1109, 1111, 1115, 1118, 1120, 1126, 1127, 1137, 1149, 1152, 1164, 1165, 1166, 1167, 1170, 1171, 1173, 1192], "positiveornegativeassoci": [3, 4, 17, 21, 23, 30, 37, 41, 43, 46, 53, 60, 65, 66, 67, 75, 76, 78, 79, 82, 84, 85, 86, 87, 90], "uriorcuri": [3, 4, 17, 20, 21, 22, 23, 24, 30, 36, 43, 44, 46, 55, 56, 60, 61, 63, 65, 69, 71, 72, 73, 74, 75, 78, 82, 84, 85, 90, 93, 119, 125, 142, 163, 212, 217, 223, 227, 228, 232, 233, 234, 245, 247, 269, 276, 279, 286, 288, 318, 328, 331, 351, 359, 437, 476, 480, 488, 503, 509, 512, 514, 521, 522, 530, 533, 535, 540, 541, 542, 545, 596, 608, 613, 668, 672, 692, 693, 707, 711, 717, 743, 765, 766, 771, 780, 787, 791, 793, 803, 816, 817, 864, 882, 936, 939, 940, 941, 942, 952, 953, 964, 991, 999, 1001, 1014, 1028, 1041, 1043, 1055, 1066, 1067], "predic": [3, 4, 17, 22, 23, 36, 38, 42, 46, 49, 51, 56, 65, 66, 71, 85, 86, 140, 153, 163, 165, 170, 171, 172, 173, 181, 188, 189, 191, 197, 199, 269, 279, 311, 316, 318, 331, 344, 352, 373, 380, 384, 386, 403, 405, 411, 412, 417, 421, 437, 450, 455, 479, 485, 551, 613, 825, 842, 857, 874, 876, 882, 888, 912, 936, 941, 953, 1035, 1043, 1060, 1067, 1099, 1100, 1102, 1106, 1107, 1108, 1110, 1113, 1114, 1117, 1118, 1119, 1124, 1128, 1131, 1135, 1145, 1156, 1162, 1165, 1166, 1167, 1172, 1175, 1177, 1178, 1192], "relationship": [3, 17, 22, 23, 41, 46, 75, 76, 140, 153, 163, 182, 212, 227, 262, 269, 276, 277, 279, 284, 286, 288, 289, 307, 318, 328, 329, 331, 347, 351, 359, 362, 384, 388, 437, 443, 446, 447, 448, 450, 462, 825, 936, 941, 952, 953, 954, 957, 1100, 1106, 1108, 1109, 1110, 1111, 1127, 1128, 1130, 1132, 1135, 1137, 1159, 1166, 1170, 1172, 1175, 1178], "ontologi": [3, 17, 22, 23, 24, 31, 41, 44, 46, 60, 67, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 158, 159, 160, 161, 164, 165, 166, 167, 168, 170, 171, 173, 174, 175, 176, 177, 179, 180, 181, 182, 183, 184, 185, 186, 188, 189, 191, 192, 193, 194, 196, 197, 198, 199, 202, 248, 262, 263, 269, 276, 277, 278, 279, 280, 281, 284, 285, 286, 287, 288, 289, 290, 307, 308, 318, 328, 329, 330, 331, 333, 334, 347, 348, 351, 356, 359, 362, 364, 372, 373, 380, 381, 382, 384, 385, 388, 389, 393, 394, 396, 403, 405, 411, 417, 418, 420, 424, 426, 427, 435, 436, 437, 441, 443, 448, 456, 464, 467, 468, 474, 475, 476, 480, 485, 488, 495, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 521, 522, 527, 530, 535, 540, 541, 542, 545, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 604, 606, 608, 609, 610, 611, 612, 617, 625, 627, 635, 640, 642, 646, 647, 655, 658, 660, 664, 665, 666, 667, 668, 672, 673, 695, 717, 728, 735, 742, 812, 813, 816, 827, 828, 839, 840, 842, 845, 847, 848, 849, 851, 852, 854, 855, 856, 857, 860, 861, 863, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 881, 882, 883, 886, 887, 888, 889, 890, 892, 893, 894, 896, 898, 899, 902, 903, 905, 907, 908, 909, 911, 912, 913, 915, 916, 917, 918, 919, 939, 941, 942, 946, 952, 953, 954, 968, 1099, 1103, 1106, 1107, 1108, 1110, 1111, 1113, 1114, 1115, 1117, 1118, 1119, 1120, 1123, 1126, 1128, 1129, 1130, 1131, 1132, 1137, 1141, 1143, 1145, 1149, 1151, 1152, 1156, 1159, 1162, 1163, 1164, 1165, 1167, 1168, 1170, 1171, 1172, 1173, 1174, 1176, 1177, 1178, 1179, 1180, 1181, 1186], "property_valu": [3, 17, 22, 23, 46, 1179], "propertyvalu": [3, 17, 22, 46, 60, 75, 79, 372, 373, 380, 381, 382, 384, 385, 388, 389, 393, 394, 396, 403, 411, 412, 417, 437, 440, 443, 450, 472, 473, 475, 1108], "pair": [3, 17, 22, 42, 46, 79, 148, 153, 157, 162, 163, 180, 183, 198, 479, 613, 638, 648, 1055, 1067, 1084, 1093, 1100, 1106, 1113, 1117, 1118, 1123, 1165, 1166, 1173, 1177, 1178], "subject_label": [3, 17, 22, 41, 46, 765, 780, 978, 988, 1001, 1110, 1114, 1129, 1135, 1165], "label": [3, 17, 22, 41, 46, 67, 76, 87, 93, 120, 125, 153, 163, 168, 171, 173, 177, 179, 182, 186, 189, 191, 194, 197, 223, 311, 321, 331, 338, 357, 363, 388, 396, 410, 412, 437, 441, 476, 478, 480, 485, 488, 501, 503, 505, 507, 509, 512, 521, 526, 529, 530, 532, 535, 540, 541, 545, 565, 598, 600, 601, 606, 613, 662, 694, 695, 717, 726, 764, 765, 773, 780, 795, 805, 813, 882, 936, 939, 940, 942, 953, 1099, 1104, 1106, 1107, 1109, 1110, 1111, 1115, 1117, 1123, 1124, 1127, 1129, 1130, 1131, 1135, 1137, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1148, 1154, 1159, 1165, 1166, 1167, 1170, 1172, 1174, 1176, 1180, 1193], "predicate_label": [3, 17, 22, 41, 46, 1110, 1135], "negat": [3, 17, 21, 22, 30, 37, 43, 46, 60, 65, 66, 67, 75, 76, 77, 78, 79, 82, 84, 85, 86, 87, 90, 1108], "evidence_typ": [3, 17, 22, 46], "evid": [3, 17, 22, 43, 46, 485, 613, 1106, 1108], "supporting_object": [3, 17, 22, 46], "aggregator_knowledge_sourc": [3, 4, 17, 21, 22, 46, 1182], "subject_closur": [3, 17, 22, 46], "via": [3, 17, 22, 46, 65, 66, 85, 86, 1099, 1102, 1105, 1106, 1108, 1109, 1113, 1114, 1116, 1117, 1120, 1129, 1135, 1136, 1155, 1162, 1165, 1173, 1176, 1192], "th": [3, 4, 17, 22, 42, 46, 381, 435, 437, 443, 453, 989, 1001], "subject_closure_label": [3, 17, 22, 46], "object_closur": [3, 17, 22, 46], "object_closure_label": [3, 17, 22, 46], "rollupgroup": [3, 32, 44, 46, 83], "pairwisecoassoci": [3, 33, 46, 57, 58, 59, 61, 62, 63, 64, 88, 1165], "associations_for_subjects_in_common": [3, 20, 46], "self": [3, 4, 17, 20, 21, 22, 23, 24, 92, 93, 94, 153, 157, 212, 213, 217, 223, 249, 250, 262, 263, 264, 265, 269, 294, 295, 307, 308, 309, 310, 311, 312, 316, 317, 318, 321, 322, 372, 373, 380, 381, 382, 384, 385, 386, 388, 389, 393, 394, 396, 402, 403, 405, 410, 411, 412, 417, 476, 479, 480, 481, 482, 483, 484, 485, 488, 489, 497, 502, 503, 504, 505, 506, 507, 508, 509, 512, 521, 522, 526, 530, 532, 533, 535, 536, 537, 540, 541, 542, 545, 677, 692, 693, 695, 696, 743, 761, 764, 765, 766, 813, 815, 816, 817, 824, 825, 827, 828, 835, 838, 839, 840, 842, 936, 939, 940, 941, 942, 978, 988, 989, 990, 991, 1028, 1035, 1040, 1041, 1043, 1046, 1047, 1048, 1049, 1050, 1055, 1058, 1059, 1060, 1167, 1172], "ontoassoc": [3, 4, 17, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 68, 69, 70, 71, 77, 79, 80, 81, 83, 85, 86, 88, 89, 90], "from_schema": [3, 4, 17, 20, 21, 22, 23, 24, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 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384, 388, 396, 405, 410, 411, 417, 436, 437, 441, 450], "websit": [373, 380, 394, 405, 411, 417, 418, 475, 1101], "weak": [373, 394, 405, 411, 417, 475, 1108], "seealso": [373, 394, 405, 411, 417, 475, 476, 480, 485, 488, 508, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 1166], "agent": [380, 480, 484, 488, 506, 509, 510, 511, 512, 521, 526, 527, 530, 532, 533, 535, 540, 541, 542, 545, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 625, 635, 646, 647, 655, 658, 664, 665, 666, 668, 816, 828, 835, 839, 840, 842, 845, 881, 882, 885, 919, 1058, 1067, 1080], "link": [380, 1035, 1065, 1067, 1068, 1069, 1072, 1073, 1076, 1077, 1084, 1085, 1086, 1092, 1093, 1096, 1106, 1110, 1114, 1118, 1131, 1156], "plai": [380, 1129], "mutual": [381, 385, 422, 423, 437, 443, 445, 458, 470, 471, 1129], "classid": [381, 437, 471], "classexpress": [381, 386, 437, 471, 483, 488, 497, 530, 536, 537, 541, 545, 556, 561, 580, 585, 613, 615, 630, 643, 645, 661, 670], "existentialrestrictionexpress": [381, 393, 422, 433, 437, 455, 460, 471], "unionequivalentto": [381, 437], "disjointunion": [381, 437, 470, 1173], "unionequivalenttoexpress": [381, 386, 437], "ot": [381, 437, 471], "predicateid": [382, 403, 437], "domainclassid": [382, 437], "rangeclassid": [382, 437], "allvaluesfromedg": [382, 384, 388, 437], "subpropertyof": [384, 388, 431, 437], "equivalentto": [384, 437], "obj": [384, 437], "head": [384, 462], "tail": [384, 447, 1140], "cliqu": [385, 388, 432, 437, 443, 445, 458, 1172], "equivalentclass": [385, 393, 488, 489, 537, 613, 628, 630, 1113, 1114, 1129, 1167, 1173], "representativenodeid": [385, 437], "cliq": [385, 437], "nodeid": [385, 437], "fstring": [386, 393], "objectsomevaluesfrom": [386, 1166, 1175], "oboidentifierstr": [388, 396, 410, 412, 436, 437], "lbl": [388, 396, 410, 412, 437], "subsetdefinit": [388, 396, 412, 436, 437, 441], "ter": [388, 437], "owlcollab": [388, 396, 400, 410, 412, 413, 418, 436, 1106], "oboformat": [388, 396, 400, 410, 412, 413, 418, 436, 1106], "legaci": [388, 396, 410, 412, 418, 441], "0008150": [388, 389, 453, 1166], "go_0008150": [388, 389, 453], "objectpropertyassert": [388, 431, 1173], "frequent": [389, 1106, 1108], "differenti": [393, 437, 460, 1113], "objectintersectionof": 393, "89": [393, 434, 460], "somevaluesfrom": [393, 460, 537, 613, 628, 1102, 1108, 1166], "affect": [394, 437], "belong": [394, 437, 464, 476, 480, 488, 502, 509, 512, 521, 530, 535, 540, 541, 545, 612, 613, 1119, 1166], "definitionpropertyvalu": [394, 405, 426, 437, 440, 443, 450, 472, 473, 475], "xrefpropertyvalu": [394, 405, 437, 440, 443, 450, 472, 473, 475], "basicpropertyvalu": [394, 405, 437, 440, 443, 450, 472, 473, 475], "predef": [394, 437], "insubset": [394, 464, 476, 480, 488, 502, 509, 512, 521, 530, 535, 540, 541, 545, 612], "versioninfo": [394, 474, 533, 613, 674, 835, 918], "histor": 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476, 480, 485, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 600, 1104, 1107, 1115], "hasnarrowsynonym": [401, 406, 476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 601, 1107], "hasbroadsynonym": [401, 406, 476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 598, 1107], "hasrelatedsynonym": [401, 406, 476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 606, 1104, 1107], "go_": [402, 437, 1166], "strongli": [402, 452], "r1": [403, 437], "rn": [403, 437], "chainpredicateid": [403, 437], "claus": [403, 421, 437], "prope": [403, 437], "broader": [406, 1106, 1129], "bu": 406, "subsetproperti": [410, 1166], "synonymtyp": [411, 412, 437, 438, 1107], "synonymtypeidentifierstr": [411, 437, 465], "isexact": [411, 437], "scopeenum": [411, 437], "commonli": [413, 1106, 1192], "plain": [413, 698, 1107], "pmid": [417, 1108, 1129], "12345": 417, "registri": [418, 1182], "bioregistri": 418, "usag": [419, 429, 437, 443, 451, 457, 1106, 1107, 1109, 1118, 1128, 1129, 1164, 1174], "propert": [419, 429, 443, 451, 457], "principl": [437, 448, 1035, 1060, 1093, 1117], "attach": [437, 448, 694, 1166, 1174], "metedata": [437, 448], "Not": [437, 448, 1117, 1140, 1157], "obographs_datamodel": 437, "expr": 437, "nodetypeenum": 437, "objec": [440, 443, 450, 472, 473, 475], "benchmark": 449, "scopesenum": 461, "namedobject": [476, 480, 485, 488, 509, 512, 521, 530, 533, 535, 540, 541, 542, 545, 552, 608, 613, 668], "hassynonym": [476, 480, 481, 485, 488, 509, 510, 511, 512, 521, 522, 527, 530, 535, 540, 541, 545, 550, 584, 598, 600, 601, 606, 613, 662], "haslifecycl": [476, 480, 481, 484, 488, 509, 512, 521, 522, 526, 530, 532, 535, 540, 541, 542, 545, 563, 578, 591, 592, 593, 596, 603, 613, 658, 665], "hasproven": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 533, 535, 540, 541, 545, 564, 566, 567, 568, 569, 572, 576, 583, 610, 613, 617, 646, 664, 666], "hasmap": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 535, 540, 541, 542, 545, 555, 559, 571, 588, 613, 635], "hascategori": [476, 480, 481, 488, 509, 512, 521, 522, 530, 535, 540, 541, 542, 545, 557, 562, 602, 612, 613], "hasuserinform": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 533, 535, 540, 541, 542, 545, 560, 570, 577, 589, 599, 609, 613, 647, 655], "hasminimalmetadata": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 535, 540, 541, 545, 575, 613, 625], "has_exact_synonym": [476, 480, 485, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613, 662], "labeltyp": [476, 480, 485, 488, 505, 507, 509, 512, 521, 530, 535, 540, 541, 545, 598, 600, 601, 606, 613, 625, 662], "has_narrow_synonym": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613, 662], "has_broad_synonym": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613, 662], "has_related_synonym": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613], "alternative_term": [476, 477, 480, 488, 507, 509, 510, 511, 512, 521, 527, 530, 535, 540, 541, 545, 584, 598, 600, 601, 613, 662], "isa_alternative_term": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 550, 613], "iedb_alternative_term": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 550, 613], "editor_preferred_term": [476, 480, 488, 507, 509, 512, 521, 528, 530, 535, 540, 541, 545, 550, 613], "obo_foundry_unique_label": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 550, 613], "has_obsolescence_reason": [476, 480, 488, 503, 509, 512, 521, 530, 532, 535, 540, 541, 545, 613, 641], "term_replaced_bi": [476, 477, 480, 484, 488, 499, 503, 509, 512, 521, 528, 530, 532, 535, 540, 541, 545, 613, 641], "has_alternative_id": [476, 480, 488, 499, 503, 509, 512, 521, 526, 530, 535, 540, 541, 545, 613, 641], "excluded_from_qc_check": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 542, 545, 590, 613], "excluded_subclassof": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 590, 613], "excluded_synonym": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 590, 613], "should_conform_to": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 542, 545, 590, 613], "created_bi": [476, 480, 485, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "creator": [476, 480, 485, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 567, 613, 650, 1174], "came": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 566, 613], "editor_not": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "narrativetext": [476, 480, 488, 505, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 575, 583, 613, 667], "term_editor": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "definition_sourc": [476, 480, 488, 506, 509, 512, 518, 521, 528, 530, 535, 540, 541, 545, 613, 650], "ontology_term_request": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "imported_from": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "term_tracker_item": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "broadmatch": [476, 480, 488, 504, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 629], "closematch": [476, 480, 488, 504, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 629, 694, 1129], "exactmatch": [476, 480, 488, 504, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 629], "narrowmatch": [476, 480, 488, 504, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 629], "database_cross_refer": [476, 480, 485, 488, 504, 509, 512, 521, 530, 535, 540, 541, 545, 613, 629], "curieliter": [476, 480, 485, 488, 504, 509, 512, 521, 530, 535, 540, 541, 545, 571, 613], "has_obo_namespac": [476, 480, 488, 502, 509, 512, 521, 530, 535, 540, 541, 545, 613], "in_subset": [476, 480, 485, 488, 502, 503, 505, 506, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 563, 575, 576, 578, 584, 589, 596, 613, 625, 665], "conformsto": [476, 480, 488, 502, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 614], "example_of_usag": [476, 477, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614], "curator_not": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "has_curation_statu": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614], "depicted_bi": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614], "page": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614, 1106, 1109], "transitiveproperti": [476, 484, 488, 510, 511, 512, 521, 526, 527, 530, 532, 533, 535, 540, 542, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 580, 582, 583, 584, 586, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 616, 617, 620, 621, 623, 624, 625, 635, 646, 647, 649, 652, 655, 657, 658, 663, 664, 665, 666, 668, 1166], "homosapien": [476, 484, 488, 510, 511, 512, 521, 526, 527, 532, 533, 540, 542, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 625, 635, 646, 647, 655, 658, 664, 665, 666, 668], "orcid": [476, 509, 1107], "omoschema": [476, 479, 480, 481, 482, 483, 484, 485, 488, 489, 495, 497, 502, 503, 504, 505, 506, 507, 508, 509, 512, 521, 522, 526, 530, 532, 533, 535, 536, 537, 540, 541, 542, 545, 554, 565, 579, 590, 591, 592, 593, 605, 608, 614, 628, 629, 630, 638, 641, 648, 650, 653, 656, 658, 674], "id_prefix": [476, 509, 936, 940, 1166], "disjoint_with": [476, 480, 485, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 600], "allotrop": [476, 477, 478, 480, 485, 488, 503, 505, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 575, 578, 589, 625, 665], "permit": [476, 480, 485, 488, 503, 506, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 563, 576, 578, 584, 589, 596, 665], "profil": [476, 480, 485, 488, 503, 505, 506, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 563, 575, 576, 578, 584, 589, 596, 625, 665, 842, 872, 882, 1110, 1116, 1118, 1178], "0001847": [476, 480, 488, 507, 509, 511, 512, 521, 530, 535, 540, 541, 545], "9991118": [476, 480, 488, 507, 509, 510, 512, 521, 530, 535, 540, 541, 545], "0000111": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 584], "uniquekei": [476, 480, 488, 507, 509, 512, 521, 527, 530, 535, 540, 541, 545], "0000589": [476, 480, 488, 507, 509, 512, 521, 527, 530, 535, 540, 541, 545], "obsoletion_related_properti": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 563, 578, 596, 603, 613, 665], "obsoleteaspect": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 563, 578, 603, 613, 665], "0000231": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 603, 1115], "isreplacedbi": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 665], "0100001": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 665, 1115, 1166], "owlc": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596], "owlapi": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 1173], "317": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596], "notobsoleteaspect": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 613], "hasalternativeid": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 1115], "excluded_axiom": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 591, 592, 593, 613, 658], "hiddensynonym": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 593], "2022": [476, 480, 485, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 567, 568, 1151], "04": [476, 480, 485, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 567, 568], "12": [476, 480, 485, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 567, 568], "deprecated_element_has_exact_replac": [476, 480, 485, 488, 506, 509, 512, 518, 519, 520, 521, 530, 535, 540, 541, 545, 567, 568, 624, 640], "provenance_properti": [476, 480, 485, 488, 506, 508, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 566, 567, 568, 569, 570, 572, 573, 576, 583, 597, 610, 613, 646, 660, 664, 666], "wasattributedto": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "structured_pattern": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "orcid_regex": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "interpol": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "partial_match": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "pav": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 566, 572, 617, 673], "createdon": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 566], "authoredon": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 572], "importedfrom": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 617], "0000116": [476, 480, 488, 506, 509, 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"Slot: itemListElements": [[237, "slot-itemlistelements"]], "Slot: itemLists": [[238, "slot-itemlists"]], "Slot: itemMetadataMap": [[239, "slot-itemmetadatamap"]], "Slot: keywords": [[240, "slot-keywords"]], "Slot: name": [[241, "slot-name"], [282, "slot-name"], [341, "slot-name"]], "Slot: numberOfItems": [[242, "slot-numberofitems"]], "Slot: position": [[243, "slot-position"]], "Slot: previousItem": [[244, "slot-previousitem"]], "Slot: type": [[245, "slot-type"], [292, "slot-type"], [369, "slot-type"], [468, "slot-type"], [668, "slot-type"], [1093, "slot-type"]], "Slot: url": [[246, "slot-url"], [671, "slot-url"], [1096, "slot-url"]], "Slot: wasGeneratedBy": [[247, "slot-wasgeneratedby"]], "KGCL": [[248, "kgcl"]], "Class: Activity": [[249, "class-activity"], [294, "class-activity"]], "Class: Any": [[250, "class-any"], [295, "class-any"], [484, "class-any"]], "Class: LexicalGrouping": [[262, "class-lexicalgrouping"], [307, "class-lexicalgrouping"]], "Class: LexicalIndex": [[263, 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"Slot: has_axiom_label": [[597, "slot-has-axiom-label"]], "Slot: has_broad_synonym": [[598, "slot-has-broad-synonym"]], "Slot: has_curation_status": [[599, "slot-has-curation-status"]], "Slot: has_exact_synonym": [[600, "slot-has-exact-synonym"]], "Slot: has_narrow_synonym": [[601, "slot-has-narrow-synonym"]], "Slot: has_obo_namespace": [[602, "slot-has-obo-namespace"]], "Slot: has_obsolescence_reason": [[603, "slot-has-obsolescence-reason"]], "Slot: has_ontology_root_term": [[604, "slot-has-ontology-root-term"]], "Slot: has_rank": [[605, "slot-has-rank"]], "Slot: has_related_synonym": [[606, "slot-has-related-synonym"]], "Slot: has_synonym_type": [[607, "slot-has-synonym-type"]], "Slot: image": [[609, "slot-image"]], "Slot: imported_from": [[610, "slot-imported-from"]], "Slot: imports": [[611, "slot-imports"]], "Slot: in_subset": [[612, "slot-in-subset"]], "Ontology Metadata Ontology Schema": [[613, "ontology-metadata-ontology-schema"]], "Slot: informative_property": [[614, 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[[632, "slot-members"]], "Slot: minCardinality": [[633, "slot-mincardinality"]], "Slot: minQualifiedCardinality": [[634, "slot-minqualifiedcardinality"]], "Slot: narrowMatch": [[635, "slot-narrowmatch"]], "Slot: never_in_taxon": [[636, "slot-never-in-taxon"]], "Slot: notes": [[637, "slot-notes"]], "Slot: oboInOwl_id": [[639, "slot-oboinowl-id"]], "Slot: oboInOwl_ontology": [[640, "slot-oboinowl-ontology"]], "Slot: obsoletion_related_property": [[641, "slot-obsoletion-related-property"]], "omo-schema": [[642, "omo-schema"]], "Slot: onClass": [[643, "slot-onclass"]], "Slot: onProperty": [[644, "slot-onproperty"]], "Slot: oneOf": [[645, "slot-oneof"]], "Slot: ontology_term_requester": [[646, "slot-ontology-term-requester"]], "Slot: page": [[647, "slot-page"]], "Slot: propertyChainAxiom": [[649, "slot-propertychainaxiom"]], "Slot: provenance_property": [[650, "slot-provenance-property"]], "Slot: qualifiedCardinality": [[651, "slot-qualifiedcardinality"]], "Slot: range": [[652, "slot-range"]], "Slot: reification_predicate": [[653, "slot-reification-predicate"]], "Slot: sameAs": [[654, "slot-sameas"]], "Slot: seeAlso": [[655, "slot-seealso"]], "Slot: shortcut_annotation_property": [[656, "slot-shortcut-annotation-property"]], "Slot: shorthand": [[657, "slot-shorthand"]], "Slot: should_conform_to": [[658, "slot-should-conform-to"]], "Slot: someValuesFrom": [[659, "slot-somevaluesfrom"]], "Slot: subClassOf": [[661, "slot-subclassof"]], "Slot: synonym": [[662, "slot-synonym"]], "Slot: temporal_interpretation": [[663, "slot-temporal-interpretation"]], "Slot: term_editor": [[664, "slot-term-editor"]], "Slot: term_replaced_by": [[665, "slot-term-replaced-by"]], "Slot: term_tracker_item": [[666, "slot-term-tracker-item"]], "Slot: title": [[667, "slot-title"], [913, "slot-title"]], "Slot: unionOf": [[670, "slot-unionof"]], "Slot: versionIRI": [[672, "slot-versioniri"]], "Slot: versionInfo": [[673, "slot-versioninfo"]], "Slot: version_property": [[674, 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"slot-object-source"], [1013, "slot-object-source"]], "Slot: object_source_version": [[729, "slot-object-source-version"]], "Slot: path_to": [[730, "slot-path-to"]], "Slot: properties": [[731, "slot-properties"]], "Slot: result_count": [[733, "slot-result-count"]], "search-datamodel": [[735, "search-datamodel"]], "Slot: search_term": [[736, "slot-search-term"]], "Slot: search_terms": [[737, "slot-search-terms"]], "Slot: snippet": [[738, "slot-snippet"]], "Slot: syntax": [[739, "slot-syntax"]], "Slot: traversal": [[740, "slot-traversal"]], "SemSQL": [[742, "semsql"]], "Class: BestMatch": [[743, "class-bestmatch"]], "Type: ItemCount": [[753, "type-itemcount"]], "Type: NegativeLogValue": [[757, "type-negativelogvalue"]], "Type: NonNegativeFloat": [[759, "type-nonnegativefloat"]], "Class: PairwiseSimilarity": [[761, "class-pairwisesimilarity"]], "Class: TermInfo": [[764, "class-terminfo"]], "Class: TermPairwiseSimilarity": [[765, "class-termpairwisesimilarity"]], "Class: 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"slot-match-subsumer"]], "Slot: match_subsumer_label": [[788, "slot-match-subsumer-label"]], "Slot: match_target": [[789, "slot-match-target"]], "Slot: match_target_label": [[790, "slot-match-target-label"]], "Slot: metric": [[791, "slot-metric"]], "Slot: object_best_matches": [[792, "slot-object-best-matches"]], "Slot: object_information_content": [[794, "slot-object-information-content"]], "Slot: object_termset": [[797, "slot-object-termset"]], "Slot: overlap_coefficient": [[798, "slot-overlap-coefficient"]], "Slot: phenodigm_score": [[799, "slot-phenodigm-score"]], "Slot: score": [[800, "slot-score"]], "Slot: similarity": [[801, "slot-similarity"]], "Slot: subject_best_matches": [[802, "slot-subject-best-matches"]], "Slot: subject_id": [[803, "slot-subject-id"], [1087, "slot-subject-id"]], "Slot: subject_information_content": [[804, "slot-subject-information-content"]], "Slot: subject_source": [[806, "slot-subject-source"], [1020, "slot-subject-source"]], "Slot: subject_termset": [[807, "slot-subject-termset"]], "Slot: subsumed_by_score": [[808, "slot-subsumed-by-score"]], "Slot: subsumes_score": [[809, "slot-subsumes-score"]], "Slot: union_count": [[811, "slot-union-count"]], "SSSOM": [[812, "sssom"], [1114, "sssom"]], "Class: ChangeTypeStatistic": [[815, "class-changetypestatistic"]], "Class: ContributorRole": [[816, "class-contributorrole"]], "Class: ContributorStatistics": [[817, "class-contributorstatistics"]], "Class: FacetStatistics": [[824, "class-facetstatistics"]], "LinkML Specification": [[824, "linkml-specification"], [827, "linkml-specification"], [838, "linkml-specification"]], "Class: FacetedCount": [[825, "class-facetedcount"]], "Class: GlobalStatistics": [[827, "class-globalstatistics"]], "Class: GroupedStatistics": [[828, "class-groupedstatistics"]], "Class: SummaryStatisticCollection": [[838, "class-summarystatisticcollection"]], "Class: SummaryStatisticsCalculationActivity": [[839, "class-summarystatisticscalculationactivity"]], "Class: SummaryStatisticsReport": [[840, "class-summarystatisticsreport"]], "Class: UngroupedStatistics": [[842, "class-ungroupedstatistics"]], "Slot: acted_on_behalf_of": [[845, "slot-acted-on-behalf-of"]], "Slot: agents": [[846, "slot-agents"]], "Slot: annotation_property_count": [[847, "slot-annotation-property-count"]], "Slot: anonymous_class_expression_count": [[848, "slot-anonymous-class-expression-count"]], "Slot: anonymous_individual_count": [[849, "slot-anonymous-individual-count"]], "Slot: by_category": [[850, "slot-by-category"]], "Slot: by_ontology": [[851, "slot-by-ontology"]], "Slot: by_subset": [[852, "slot-by-subset"]], "Slot: by_taxon": [[853, "slot-by-taxon"]], "Slot: change_summary": [[854, "slot-change-summary"]], "Slot: class_count": [[855, "slot-class-count"]], "Slot: class_count_by_category": [[856, "slot-class-count-by-category"]], "Slot: class_count_by_subset": [[857, "slot-class-count-by-subset"]], "Slot: class_count_excluding_deprecated": [[858, "slot-class-count-excluding-deprecated"]], "Slot: class_count_with_definitions": [[859, "slot-class-count-with-definitions"]], "Slot: class_count_with_text_definitions": [[860, "slot-class-count-with-text-definitions"]], "Slot: class_count_without_text_definitions": [[861, "slot-class-count-without-text-definitions"]], "Slot: class_statistic_group": [[862, "slot-class-statistic-group"]], "Slot: compared_with": [[863, "slot-compared-with"]], "Slot: contributor_id": [[864, "slot-contributor-id"]], "Slot: contributor_name": [[865, "slot-contributor-name"]], "Slot: contributor_summary": [[866, "slot-contributor-summary"]], "Slot: count_statistic": [[867, "slot-count-statistic"]], "Slot: datatype_property_count": [[868, "slot-datatype-property-count"]], "Slot: deprecated_class_count": [[869, "slot-deprecated-class-count"]], "Slot: deprecated_object_property_count": [[870, "slot-deprecated-object-property-count"]], "Slot: description_logic_profile": [[872, "slot-description-logic-profile"]], "Slot: distinct_synonym_count": [[873, "slot-distinct-synonym-count"]], "Slot: edge_count_by_predicate": [[874, "slot-edge-count-by-predicate"]], "Slot: ended_at_time": [[875, "slot-ended-at-time"]], "Slot: entailed_edge_count_by_predicate": [[876, "slot-entailed-edge-count-by-predicate"]], "Slot: equivalent_classes_axiom_count": [[877, "slot-equivalent-classes-axiom-count"]], "Slot: equivalentclasses_axiom_count": [[878, "slot-equivalentclasses-axiom-count"]], "Slot: facet": [[879, "slot-facet"]], "Slot: filtered_count": [[880, "slot-filtered-count"]], "Summary Statistics Datamodel": [[882, "summary-statistics-datamodel"]], "Slot: individual_count": [[883, "slot-individual-count"]], "Slot: individual_statistic_group": [[884, "slot-individual-statistic-group"]], "Slot: mapping_count": [[886, "slot-mapping-count"]], "Slot: mapping_statement_count_by_object_source": [[887, "slot-mapping-statement-count-by-object-source"]], "Slot: mapping_statement_count_by_predicate": [[888, "slot-mapping-statement-count-by-predicate"]], "Slot: mapping_statement_count_subject_by_object_source": [[889, "slot-mapping-statement-count-subject-by-object-source"]], "Slot: merged_class_count": [[890, "slot-merged-class-count"]], "Slot: metadata_statistic_group": [[891, "slot-metadata-statistic-group"]], "Slot: named_individual_count": [[892, "slot-named-individual-count"]], "Slot: non_deprecated_class_count": [[893, "slot-non-deprecated-class-count"]], "Slot: non_deprecated_object_property_count": [[894, "slot-non-deprecated-object-property-count"]], "Slot: normalization_comments": [[895, "slot-normalization-comments"]], "Slot: object_property_count": [[896, "slot-object-property-count"]], "Slot: ontologies": [[897, "slot-ontologies"]], "Slot: ontology_count": [[898, "slot-ontology-count"]], "Slot: owl_axiom_count": [[899, "slot-owl-axiom-count"]], "Slot: owl_statistic_group": [[900, "slot-owl-statistic-group"]], "Slot: partitions": [[901, "slot-partitions"]], "Slot: property_count": [[903, "slot-property-count"]], "Slot: property_statistic_group": [[904, "slot-property-statistic-group"]], "Slot: rdf_triple_count": [[905, "slot-rdf-triple-count"]], "Slot: role_counts": [[906, "slot-role-counts"]], "Slot: started_at_time": [[907, "slot-started-at-time"]], "Slot: subclass_of_axiom_count": [[908, "slot-subclass-of-axiom-count"]], "Slot: subset_count": [[909, "slot-subset-count"]], "summary-statistics": [[910, "summary-statistics"]], "Slot: synonym_statement_count": [[911, "slot-synonym-statement-count"]], "Slot: synonym_statement_count_by_predicate": [[912, "slot-synonym-statement-count-by-predicate"]], "Slot: unsatisfiable_class_count": [[915, "slot-unsatisfiable-class-count"]], "Slot: untyped_entity_count": [[916, "slot-untyped-entity-count"]], "Slot: version_info": [[918, "slot-version-info"]], "Slot: was_associated_with": [[919, "slot-was-associated-with"]], "Slot: was_generated_by": [[920, "slot-was-generated-by"]], "Enum: ConfigurationOption": [[922, "enum-configurationoption"]], "Class: PredicateTerm": [[936, "class-predicateterm"]], "Class: SubjectTerm": [[939, "class-subjectterm"]], "Class: Taxon": [[940, "class-taxon"]], "Class: TaxonConstraint": [[941, "class-taxonconstraint"]], "Slot: asserted": [[946, "slot-asserted"]], "Slot: candidate": [[947, "slot-candidate"]], "Slot: contradicted_by": [[949, "slot-contradicted-by"]], "Slot: evolutionary": [[951, "slot-evolutionary"]], "Taxon Constraints Reporting Datamodel": [[953, "taxon-constraints-reporting-datamodel"]], "Slot: never_in": [[955, "slot-never-in"]], "Slot: only_in": [[956, "slot-only-in"]], "Slot: predicates": [[958, "slot-predicates"]], "Slot: present_in": [[959, "slot-present-in"]], "Slot: present_in_ancestor_of": [[960, "slot-present-in-ancestor-of"]], "Slot: redundant": [[961, "slot-redundant"]], "Slot: redundant_with": [[962, "slot-redundant-with"]], "Slot: redundant_with_only_in": [[963, "slot-redundant-with-only-in"]], "Slot: sources": [[964, "slot-sources"], [1017, "slot-sources"]], "Slot: taxon": [[966, "slot-taxon"]], "Slot: unsatisfiable": [[968, "slot-unsatisfiable"]], "Slot: via_terms": [[969, "slot-via-terms"]], "Class: HasSpan": [[978, "class-hasspan"]], "Class: TextAnnotation": [[988, "class-textannotation"]], "Class: TextAnnotationConfiguration": [[989, "class-textannotationconfiguration"]], "Class: TextAnnotationResultSet": [[990, "class-textannotationresultset"]], "Class: TextualElement": [[991, "class-textualelement"]], "Slot: confidence": [[998, "slot-confidence"], [1063, "slot-confidence"]], "Text Annotator Datamodel": [[1001, "text-annotator-datamodel"]], "Slot: info": [[1002, "slot-info"], [1068, "slot-info"]], "Slot: is_longest_match": [[1003, "slot-is-longest-match"]], "Slot: match_string": [[1005, "slot-match-string"]], "Slot: match_type": [[1006, "slot-match-type"]], "Slot: matches_whole_text": [[1007, "slot-matches-whole-text"]], "Slot: model": [[1008, "slot-model"]], "Slot: object_aliases": [[1009, "slot-object-aliases"]], "Slot: object_categories": [[1010, "slot-object-categories"]], "Slot: parent_document": [[1014, "slot-parent-document"]], "Slot: source_text": [[1016, "slot-source-text"]], "Slot: subject_end": [[1018, "slot-subject-end"]], "Slot: subject_start": [[1021, "slot-subject-start"]], "Slot: subject_text_id": [[1022, "slot-subject-text-id"]], "Slot: text": [[1023, "slot-text"]], "text-annotator": [[1024, "text-annotator"]], "Slot: token_exclusion_list": [[1025, "slot-token-exclusion-list"]], "Class: ConstraintComponent": [[1028, "class-constraintcomponent"]], "Class: ExternalReferenceValidationResult": [[1035, "class-externalreferencevalidationresult"]], "Class: MappingValidationResult": [[1040, "class-mappingvalidationresult"]], "Class: NamedResource": [[1041, "class-namedresource"]], "Class: RepairConfiguration": [[1046, "class-repairconfiguration"]], "Class: RepairOperation": [[1047, "class-repairoperation"]], "Class: RepairReport": [[1048, "class-repairreport"]], "Class: Report": [[1049, "class-report"]], "Class: Result": [[1050, "class-result"]], "Enum: SeverityOptions": [[1051, "enum-severityoptions"]], "Class: TypeSeverityKeyValue": [[1055, "class-typeseveritykeyvalue"]], "Class: ValidationConfiguration": [[1058, "class-validationconfiguration"]], "Class: ValidationReport": [[1059, "class-validationreport"]], "Class: ValidationResult": [[1060, "class-validationresult"]], "Enum: ValidationResultType": [[1061, "enum-validationresulttype"]], "Slot: dry_run": [[1064, "slot-dry-run"]], "Slot: http_response_code": [[1065, "slot-http-response-code"]], "Validation Results Datamodel": [[1067, "validation-results-datamodel"]], "Slot: instantiates": [[1069, "slot-instantiates"]], "Slot: max_number_results_per_type": [[1070, "slot-max-number-results-per-type"]], "Slot: modified": [[1071, "slot-modified"]], "Slot: number_of_attempts": [[1072, "slot-number-of-attempts"]], "Slot: object_info": [[1075, "slot-object-info"]], "Slot: object_str": [[1076, "slot-object-str"]], "Slot: problem": [[1079, "slot-problem"]], "Slot: prompt_info": [[1080, "slot-prompt-info"]], "Slot: repairs": [[1081, "slot-repairs"]], "Slot: schema_path": [[1083, "slot-schema-path"]], "Slot: severity": [[1084, "slot-severity"]], "Slot: subject_info": [[1088, "slot-subject-info"]], "Slot: successful": [[1089, "slot-successful"]], "Slot: suggested_modifications": [[1090, "slot-suggested-modifications"]], "Slot: suggested_predicate": [[1091, "slot-suggested-predicate"]], "Slot: time_checked": [[1092, "slot-time-checked"]], "Slot: type_severity_map": [[1094, "slot-type-severity-map"]], "Slot: validation_configuration": [[1097, "slot-validation-configuration"]], "validaton-results": [[1098, "validaton-results"]], "FAQ: Architecture and Design": [[1099, "faq-architecture-and-design"]], "What is an interface?": [[1099, "what-is-an-interface"]], "What is a Data Model?": [[1099, "what-is-a-data-model"]], "What is an iterator and why does OAK use them so much?": [[1099, "what-is-an-iterator-and-why-does-oak-use-them-so-much"]], "FAQ: Command Line": [[1100, "faq-command-line"]], "How do I see a list of commands?": [[1100, "how-do-i-see-a-list-of-commands"]], "How do I get help on a command?": [[1100, "how-do-i-get-help-on-a-command"]], "How do I get more examples of command line usage?": [[1100, "how-do-i-get-more-examples-of-command-line-usage"]], "I want to query an ontology, what do I pass for the --input option?": [[1100, "i-want-to-query-an-ontology-what-do-i-pass-for-the-input-option"]], "Why do I get a \u201cno such option\u201d error when I pass the \u201c\u2013input\u201d option?": [[1100, "why-do-i-get-a-no-such-option-error-when-i-pass-the-input-option"]], "What do the codes \u201ci\u201d and \u201cp\u201d mean?": [[1100, "what-do-the-codes-i-and-p-mean"]], "Can I pass a list of IDs (CURIEs) as input to a command?": [[1100, "can-i-pass-a-list-of-ids-curies-as-input-to-a-command"]], "Can I pass entity labels as command inputs?": [[1100, "can-i-pass-entity-labels-as-command-inputs"]], "Can I pass lexical queries as command inputs?": [[1100, "can-i-pass-lexical-queries-as-command-inputs"]], "Can I pass the results of graph queries as command inputs?": [[1100, "can-i-pass-the-results-of-graph-queries-as-command-inputs"]], "Can I make boolean combinations of query terms?": [[1100, "can-i-make-boolean-combinations-of-query-terms"]], "Can I chain commands together, unix-style?": [[1100, "can-i-chain-commands-together-unix-style"]], "What does the symbol @ mean in a query term list": [[1100, "what-does-the-symbol-mean-in-a-query-term-list"]], "Can I use the command line to visualize a subgraph?": [[1100, "can-i-use-the-command-line-to-visualize-a-subgraph"]], "Is there an over-arching philosophy or set of design principles to the OAK command line?": [[1100, "is-there-an-over-arching-philosophy-or-set-of-design-principles-to-the-oak-command-line"]], "The command isn\u2019t working the way I expected - how do I get help?": [[1100, "the-command-isn-t-working-the-way-i-expected-how-do-i-get-help"]], "FAQ: Contributing": [[1101, "faq-contributing"]], "How can I contribute?": [[1101, "how-can-i-contribute"]], "How do I stay involved?": [[1101, "how-do-i-stay-involved"]], "FAQ: General": [[1102, "faq-general"]], "What is OAK?": [[1102, "what-is-oak"]], "Are there any tutorials for OAK?": [[1102, "are-there-any-tutorials-for-oak"]], "Are there runnable examples of how to use OAK?": [[1102, "are-there-runnable-examples-of-how-to-use-oak"]], "I am familiar with both Python and Ontologies. Where should I start?": [[1102, "i-am-familiar-with-both-python-and-ontologies-where-should-i-start"]], "I find ontologies confusing. Is there a general guide to help me?": [[1102, "i-find-ontologies-confusing-is-there-a-general-guide-to-help-me"]], "Why is it called OAK?": [[1102, "why-is-it-called-oak"]], "How do I install OAK?": [[1102, "how-do-i-install-oak"]], "Can I use OAK if I don\u2019t know Python?": [[1102, "can-i-use-oak-if-i-don-t-know-python"]], "Can I contribute to OAK?": [[1102, "can-i-contribute-to-oak"]], "Is OAK just for bio-ontologies?": [[1102, "is-oak-just-for-bio-ontologies"]], "Can OAK access ontologies in ontology portals such as MatPortal or BioPortal?": [[1102, "can-oak-access-ontologies-in-ontology-portals-such-as-matportal-or-bioportal"]], "Can OAK access ontologies in triplestores such as OntoBee or Ubergraph?": [[1102, "can-oak-access-ontologies-in-triplestores-such-as-ontobee-or-ubergraph"]], "Can OAK access local files?": [[1102, "can-oak-access-local-files"]], "Can OAK access OBO Format files?": [[1102, "can-oak-access-obo-format-files"]], "Does OAK support all of OWL?": [[1102, "does-oak-support-all-of-owl"]], "Does OAK support reasoning?": [[1102, "does-oak-support-reasoning"]], "Can I use OAK to do graph queries over ontologies?": [[1102, "can-i-use-oak-to-do-graph-queries-over-ontologies"]], "Can I use OAK to do lexical search?": [[1102, "can-i-use-oak-to-do-lexical-search"]], "Can I use OAK as a text annotator?": [[1102, "can-i-use-oak-as-a-text-annotator"]], "FAQ": [[1103, "faq"]], "FAQ: Ontologies": [[1104, "faq-ontologies"]], "What is an ontology?": [[1104, "what-is-an-ontology"]], "Do we need ontologies now we have ChatGPT?": [[1104, "do-we-need-ontologies-now-we-have-chatgpt"]], "What is OWL?": [[1104, "what-is-owl"]], "What is OBO Format?": [[1104, "what-is-obo-format"]], "What is OBO": [[1104, "what-is-obo"]], "What\u2019s a synonym and how do I access them?": [[1104, "what-s-a-synonym-and-how-do-i-access-them"]], "Ancestor statistics": [[1104, "id2"], [1129, "id2"], [1135, "id1"]], "FAQ: Troubleshooting": [[1105, "faq-troubleshooting"]], "Why do I get a \u201cError: No such option: -i\u201d message": [[1105, "why-do-i-get-a-error-no-such-option-i-message"]], "How do I get a BioPortal API key?": [[1105, "how-do-i-get-a-bioportal-api-key"]], "My OBO Format file won\u2019t parse": [[1105, "my-obo-format-file-won-t-parse"]], "My OWL file takes too long to load": [[1105, "my-owl-file-takes-too-long-to-load"]], "My cached SQLite ontology is out of date": [[1105, "my-cached-sqlite-ontology-is-out-of-date"]], "I don\u2019t understand the interface/method I want to use": [[1105, "i-don-t-understand-the-interface-method-i-want-to-use"]], "Glossary": [[1106, "glossary"]], "Aliases and Synonyms": [[1107, "aliases-and-synonyms"]], "Use Cases": [[1107, "use-cases"]], "Search": [[1107, "search"], [1129, "search"], [1149, "search"], [1163, "search"]], "Text mining and NLP": [[1107, "text-mining-and-nlp"]], "Different aliases for different communities": [[1107, "different-aliases-for-different-communities"]], "Different Languages": [[1107, "different-languages"]], "Different approaches to representing synonym metadata": [[1107, "different-approaches-to-representing-synonym-metadata"]], "Representation of synonyms in OAK": [[1107, "representation-of-synonyms-in-oak"]], "Simple Core Model": [[1107, "simple-core-model"]], "HPO basic aliases": [[1107, "id1"]], "Obo Graph Data Model": [[1107, "obo-graph-data-model"]], "HPO full aliases": [[1107, "id2"]], "Associations and Curated Annotations": [[1108, "associations-and-curated-annotations"]], "Background": [[1108, "background"], [1118, "background"]], "Association support in OAK": [[1108, "association-support-in-oak"]], "Data Model": [[1108, "data-model"], [1118, "data-model"], [1171, "data-model"]], "Selecting association sources": [[1108, "selecting-association-sources"]], "Further reading": [[1108, "further-reading"], [1110, "further-reading"], [1113, "further-reading"], [1114, "further-reading"], [1116, "further-reading"], [1118, "further-reading"]], "OAK Basics": [[1109, "oak-basics"]], "What is an ontology and why would I want to access one?": [[1109, "what-is-an-ontology-and-why-would-i-want-to-access-one"]], "Ontology languages, standards, and formats": [[1109, "ontology-languages-standards-and-formats"]], "Core OAK concepts": [[1109, "core-oak-concepts"]], "Identifying entities: CURIEs and URIs": [[1110, "curies-and-uris"]], "Prefix maps": [[1110, "prefix-maps"]], "Querying prefixmaps": [[1110, "querying-prefixmaps"]], "Example prefixes": [[1110, "id1"]], "Non-default prefixmaps": [[1110, "non-default-prefixmaps"]], "Structure of identifiers": [[1110, "structure-of-identifiers"]], "The OAK Guide": [[1111, "the-oak-guide"]], "Learning More": [[1112, "learning-more"]], "Logical Definitions": [[1113, "logical-definitions"]], "Logical Definitions in OWL": [[1113, "logical-definitions-in-owl"]], "Genus-differentia form logical definitions": [[1113, "genus-differentia-form-logical-definitions"]], "The Obo Graphs Model": [[1113, "the-obo-graphs-model"]], "Querying for logical definitions in OAK": [[1113, "querying-for-logical-definitions-in-oak"]], "uberon nail logical definitions": [[1113, "id2"]], "Reasoning using logical definitions": [[1113, "reasoning-using-logical-definitions"]], "Logical definitions and design patterns": [[1113, "logical-definitions-and-design-patterns"]], "Generating logical definitions": [[1113, "generating-logical-definitions"]], "Analyzing logical definitions": [[1113, "analyzing-logical-definitions"]], "Validating logical definitions": [[1113, "validating-logical-definitions"]], "Mappings and Cross-References": [[1114, "mappings-and-cross-references"]], "Mappings in OAK": [[1114, "mappings-in-oak"]], "uberon sssom mappings": [[1114, "id1"]], "In Python": [[1114, "in-python"]], "Generating Mappings": [[1114, "generating-mappings"]], "Obsoletion": [[1115, "obsoletion"]], "Looking up obsoleted entities": [[1115, "looking-up-obsoleted-entities"]], "Conventions and standards": [[1115, "conventions-and-standards"]], "obsolete entities should not be in the signature of any logical axiom": [[1115, "obsolete-entities-should-not-be-in-the-signature-of-any-logical-axiom"]], "obsolete entities should be accompanied by metadata that provides additional context for humans and machines": [[1115, "obsolete-entities-should-be-accompanied-by-metadata-that-provides-additional-context-for-humans-and-machines"]], "Merged entities": [[1115, "merged-entities"]], "Further Reading": [[1115, "further-reading"]], "Primary Labels": [[1116, "primary-labels"]], "Looking up labels": [[1116, "looking-up-labels"]], "Custom label annotation properties": [[1116, "custom-label-annotation-properties"]], "Multilingual ontologies": [[1116, "multilingual-ontologies"]], "Other edge cases": [[1116, "other-edge-cases"]], "Relationships and Graphs": [[1117, "relationships-and-graphs"]], "Exploring relationships": [[1117, "exploring-relationships"]], "Graph Traversal and Relation Graph Reasoning": [[1117, "graph-traversal-and-relation-graph-reasoning"]], "Graph Traversal Strategies": [[1117, "graph-traversal-strategies"]], "Examples of where entailment yields more": [[1117, "examples-of-where-entailment-yields-more"]], "Examples of where graph traversal yields more ancestors than entailment": [[1117, "examples-of-where-graph-traversal-yields-more-ancestors-than-entailment"]], "Which strategy should I use?": [[1117, "which-strategy-should-i-use"]], "A note on entailed direct edges": [[1117, "a-note-on-entailed-direct-edges"]], "Computing Similarity between Entities": [[1118, "computing-similarity-between-entities"]], "Concepts": [[1118, "concepts"]], "Jaccard Similarity": [[1118, "jaccard-similarity"]], "Information Content": [[1118, "information-content"]], "Aggregate measures for comparing entities": [[1118, "aggregate-measures-for-comparing-entities"]], "Vector-based approaches": [[1118, "vector-based-approaches"]], "Implementations": [[1118, "implementations"], [1140, "implementations"], [1152, "implementations"]], "Default Implementation": [[1118, "default-implementation"]], "Ubergraph": [[1118, "ubergraph"], [1131, "ubergraph"]], "Semsimian": [[1118, "semsimian"]], "FHIR Conversions": [[1119, "fhir-conversions"]], "CLI": [[1119, "cli"]], "Config file": [[1119, "config-file"]], "How-To Guides": [[1120, "how-to-guides"]], "How to use Large Language Models (LLMs) with OAK": [[1123, "how-to-use-large-language-models-llms-with-oak"]], "LLM frameworks that use OAK": [[1123, "llm-frameworks-that-use-oak"]], "OntoGPT": [[1123, "ontogpt"]], "CurateGPT": [[1123, "curategpt"]], "Talisman": [[1123, "talisman"]], "Using OAK in conjunction with existing LLM tools": [[1123, "using-oak-in-conjunction-with-existing-llm-tools"]], "OAK LLM Adapter": [[1123, "oak-llm-adapter"]], "Annotation": [[1123, "annotation"], [1151, "annotation"], [1153, "annotation"], [1158, "annotation"]], "Suggesting Definitions": [[1123, "suggesting-definitions"]], "Validating Mappings": [[1123, "validating-mappings"]], "Selecting alternative models": [[1123, "selecting-alternative-models"]], "Installing LLM plugins": [[1123, "installing-llm-plugins"]], "Mixtral via Ollama and LiteLLM": [[1123, "mixtral-via-ollama-and-litellm"]], "Mixtral via groq and LiteLLM": [[1123, "mixtral-via-groq-and-litellm"]], "How to Validate an OBO ontology using Obo Metadata Ontology schema": [[1124, "how-to-validate-an-obo-ontology-using-obo-metadata-ontology-schema"]], "Steps": [[1124, "steps"]], "Step 1: Obtain the sqlite version of the ontology": [[1124, "step-1-obtain-the-sqlite-version-of-the-ontology"]], "Step 2: Install oaklib": [[1124, "step-2-install-oaklib"]], "Step 3: Validate an individual ontology": [[1124, "step-3-validate-an-individual-ontology"]], "Step 3 (alternative): Validate multiple ontologies": [[1124, "step-3-alternative-validate-multiple-ontologies"]], "Caveats": [[1124, "caveats"]], "Using your own schema": [[1124, "using-your-own-schema"]], "How this works": [[1124, "how-this-works"], [1133, "how-this-works"]], "Analysis": [[1124, "analysis"]], "How to write a plugin": [[1126, "how-to-write-a-plugin"]], "What is a plugin?": [[1126, "what-is-a-plugin"]], "An example plugin": [[1126, "an-example-plugin"]], "Creating a plugin": [[1126, "creating-a-plugin"]], "Discuss on the issue tracker": [[1126, "discuss-on-the-issue-tracker"]], "Create a new project": [[1126, "create-a-new-project"], [1130, "create-a-new-project"]], "Implement one or more interfaces": [[1126, "implement-one-or-more-interfaces"]], "Implement a selector": [[1126, "implement-a-selector"]], "Write tests": [[1126, "write-tests"]], "Ontology Access Kit (OAK) Documentation": [[1127, "ontology-access-kit-oak-documentation"]], "Indices and tables": [[1127, "indices-and-tables"]], "Tutorial": [[1128, "tutorial"]], "Part 1: Getting Started": [[1129, "part-1-getting-started"]], "Installation": [[1129, "installation"]], "Install from PyPI": [[1129, "install-from-pypi"]], "Run the OAK command": [[1129, "run-the-oak-command"]], "Basics": [[1129, "basics"]], "Query the OBO Library": [[1129, "query-the-obo-library"]], "Working with local files": [[1129, "working-with-local-files"]], "Introduction to graphs and trees": [[1129, "introduction-to-graphs-and-trees"]], "Fetching ancestors": [[1129, "fetching-ancestors"]], "Predicate Abbreviations": [[1129, "predicate-abbreviations"]], "Ancestor Statistics": [[1129, "ancestor-statistics"]], "Oak Trees": [[1129, "oak-trees"]], "Advanced Search": [[1129, "advanced-search"]], "Using search terms as parameters": [[1129, "using-search-terms-as-parameters"]], "Chaining Commands": [[1129, "chaining-commands"]], "Visualization": [[1129, "visualization"]], "Using other backends": [[1129, "using-other-backends"]], "Using Ubergraph": [[1129, "using-ubergraph"]], "Using Ontobee": [[1129, "using-ontobee"]], "Using BioPortal and OntoPortal": [[1129, "using-bioportal-and-ontoportal"]], "Annotate results": [[1129, "id3"]], "Using OLS": [[1129, "using-ols"]], "OLS SSSOM": [[1129, "id4"]], "Next steps": [[1129, "next-steps"]], "Part 2: Basic Python": [[1130, "part-2-basic-python"]], "Install Poetry": [[1130, "install-poetry"]], "Basic Concepts": [[1130, "basic-concepts"]], "Code the first example": [[1130, "code-the-first-example"]], "Extending the example": [[1130, "extending-the-example"]], "Part 3: Triplestore Backends": [[1131, "part-3-triplestore-backends"]], "Triplestore Concepts": [[1131, "triplestore-concepts"]], "Connecting": [[1131, "connecting"], [1163, "connecting"]], "Basic Operations": [[1131, "basic-operations"]], "Relationships": [[1131, "relationships"]], "Part 4: OboGraphs": [[1132, "part-4-obographs"]], "OboGraphs": [[1132, "obographs"]], "OboGraph Interface": [[1132, "obograph-interface"], [1172, "obograph-interface"]], "Code examples": [[1132, "code-examples"]], "Part 5: Graph Visualization": [[1133, "part-5-graph-visualization"]], "Install Graphviz": [[1133, "install-graphviz"]], "Install OBOGraphViz": [[1133, "install-obographviz"]], "Command Line Usage": [[1133, "command-line-usage"], [1143, "command-line-usage"], [1148, "command-line-usage"]], "Programmatic usage": [[1133, "programmatic-usage"]], "Part 6: Working With OWL": [[1134, "part-6-working-with-owl"]], "OWL Datamodel": [[1134, "owl-datamodel"]], "OwlInterface": [[1134, "owlinterface"]], "ROBOT Plugin": [[1134, "robot-plugin"]], "Part 7: SQLite files": [[1135, "part-7-sqlite-files"]], "Download a SQLite file": [[1135, "download-a-sqlite-file"]], "Example": [[1135, "example"]], "Fetching ready-made SQLite files": [[1135, "fetching-ready-made-sqlite-files"]], "Building your own SQLite files": [[1135, "building-your-own-sqlite-files"]], "With docker": [[1135, "with-docker"]], "Without docker": [[1135, "without-docker"]], "Validating an ontology": [[1135, "validating-an-ontology"]], "Other RDBMSs": [[1135, "other-rdbmss"]], "Python ORM": [[1135, "python-orm"]], "Part 8: Applying Changes to Ontologies": [[1136, "part-8-applying-changes-to-ontologies"]], "About KGCL": [[1136, "about-kgcl"]], "Example: Sqlite3": [[1136, "example-sqlite3"]], "Example: OBO Files": [[1136, "example-obo-files"]], "Introduction": [[1137, "introduction"]], "Basic Python Example": [[1137, "basic-python-example"]], "Basic Command Line Example": [[1137, "basic-command-line-example"]], "Jupyter Notebooks": [[1139, "jupyter-notebooks"]], "Architecture": [[1140, "architecture"]], "Ontology Interfaces": [[1140, "ontology-interfaces"]], "Other Interfaces": [[1140, "other-interfaces"]], "Example: OWL Ontology Interface": [[1140, "example-owl-ontology-interface"]], "Partial and Complete Implementation": [[1140, "partial-and-complete-implementation"]], "Best Practice": [[1141, "best-practice"]], "External Services": [[1141, "external-services"]], "Iterators": [[1141, "iterators"]], "Weaving calls together": [[1141, "weaving-calls-together"]], "Chunking": [[1141, "chunking"]], "Abstract Class": [[1142, "abstract-class"]], "Converters": [[1143, "converters"]], "Converting from Obo Graphs": [[1143, "converting-from-obo-graphs"]], "OBO Graph to CX Converter": [[1144, "obo-graph-to-cx-converter"]], "OBO Graph to FHIR Converter": [[1145, "obo-graph-to-fhir-converter"]], "OBO Graph to OBO Format Converter": [[1146, "obo-graph-to-obo-format-converter"]], "OBO Graph to OWL Converter": [[1147, "obo-graph-to-owl-converter"]], "Aggregator Adapter": [[1148, "aggregator-adapter"]], "Documentation": [[1148, "documentation"], [1156, "documentation"]], "Bioportal Adapter": [[1149, "bioportal-adapter"]], "API Keys": [[1149, "api-keys"]], "Command Line Examples": [[1149, "command-line-examples"], [1151, "command-line-examples"], [1153, "command-line-examples"], [1158, "command-line-examples"]], "Code": [[1149, "code"], [1151, "code"], [1153, "code"], [1154, "code"], [1155, "code"], [1157, "code"], [1158, "code"], [1159, "code"], [1160, "code"], [1161, "code"], [1162, "code"], [1163, "code"]], "FunOwl Adapter": [[1150, "funowl-adapter"]], "Gilda Adapter": [[1151, "gilda-adapter"]], "LLM Adapter": [[1153, "llm-adapter"]], "OBO Graph Adapter": [[1154, "obo-graph-adapter"]], "About": [[1154, "about"], [1157, "about"], [1159, "about"], [1160, "about"], [1163, "about"]], "Initialization": [[1154, "initialization"], [1159, "initialization"], [1160, "initialization"], [1162, "initialization"]], "Ontology Lookup Service (OLS) Adapter": [[1155, "ontology-lookup-service-ols-adapter"]], "Ontobee Adapter": [[1156, "ontobee-adapter"]], "Notes": [[1156, "notes"]], "Owlery Adapter": [[1157, "owlery-adapter"]], "PantherDB Adapter": [[1158, "pantherdb-adapter"]], "Enrichment": [[1158, "enrichment"]], "Mapping": [[1158, "mapping"]], "Pronto / OBO Files Adapter": [[1159, "pronto-obo-files-adapter"]], "Input Selector": [[1159, "input-selector"]], "Simple OBO Adapter": [[1160, "simple-obo-adapter"]], "Sparql Adapter": [[1161, "sparql-adapter"]], "SQL Database Adapter": [[1162, "sql-database-adapter"]], "SQL Alchemy ORM Model": [[1162, "sql-alchemy-orm-model"]], "Ubergraph Adapter": [[1163, "ubergraph-adapter"]], "Interfaces Implemented": [[1163, "interfaces-implemented"]], "OAK Library Documentation": [[1164, "oak-library-documentation"]], "Association Provider Interface": [[1165, "association-provider-interface"]], "Command Line Use": [[1165, "command-line-use"], [1171, "command-line-use"]], "Basic Ontology Interface": [[1166, "basic-ontology-interface"]], "Class Enrichment Calculation Interface": [[1167, "class-enrichment-calculation-interface"]], "Differ Interface": [[1168, "differ-interface"]], "Dumper Interface": [[1169, "dumper-interface"]], "Interfaces": [[1170, "interfaces"]], "Mapping Provider Interface": [[1171, "mapping-provider-interface"]], "OWL Interface": [[1173, "owl-interface"]], "Patcher Interface": [[1174, "patcher-interface"]], "Relation Graph": [[1175, "relation-graph"]], "Search Interface": [[1176, "search-interface"]], "Semantic Similarity Interface": [[1177, "semantic-similarity-interface"]], "Subsetting": [[1178, "subsetting"]], "Summary Statistics": [[1179, "summary-statistics"]], "Text Annotator Interface": [[1180, "text-annotator-interface"]], "Validator Interface": [[1181, "validator-interface"]], "Ontology Adapter Selectors": [[1182, "ontology-adapter-selectors"]], "Syntax": [[1182, "syntax"]], "Schemes": [[1182, "schemes"]], "pronto": [[1182, "pronto"]], "prontolib": [[1182, "prontolib"]], "sqlite": [[1182, "sqlite"]], "obosqlite": [[1182, "obosqlite"]], "ontobee": [[1182, "ontobee"]], "ols": [[1182, "ols"]], "bioportal": [[1182, "bioportal"]], "funowl": [[1182, "funowl"]], "Functions": [[1182, "functions"]], "oaklib.utilities.apikey_manager": [[1183, "module-oaklib.utilities.apikey_manager"]], "oaklib.utilities.graph.networkx_bridge": [[1184, "module-oaklib.utilities.graph.networkx_bridge"]], "Utilities for working with networkx": [[1184, "utilities-for-working-with-networkx"]], "oaklib.utilities.graph.relationship_walker": [[1185, "module-oaklib.utilities.graph.relationship_walker"]], "Utilities for traversing Ontology Graphs": [[1185, "utilities-for-traversing-ontology-graphs"]], "oaklib.utilities.lexical.lexical_indexer": [[1186, "module-oaklib.utilities.lexical.lexical_indexer"]], "Lexical Utilities": [[1186, "lexical-utilities"]], "oaklib.utilities.obograph_utils": [[1187, "module-oaklib.utilities.obograph_utils"]], "Utilities for the OBOGraph Datamodel": [[1187, "utilities-for-the-obograph-datamodel"]], "oaklib.utilities.subsets.slimmer_utils": [[1188, "module-oaklib.utilities.subsets.slimmer_utils"]], "Utilities for working with ontology subsets (slims)": [[1188, "utilities-for-working-with-ontology-subsets-slims"]], "oaklib.utilities.table_filler": [[1189, "module-oaklib.utilities.table_filler"]], "oaklib.utilities.taxon": [[1190, "module-oaklib.utilities.taxon"]], "Utilities": [[1191, "utilities"]], "Layering on RDF/OWL": [[1192, "layering-on-rdf-owl"]], "CURIEs, URIs, and prefixmaps": [[1192, "curies-uris-and-prefixmaps"]], "Relationships between entities": [[1192, "relationships-between-entities"]], "Metadata about entities": [[1192, "metadata-about-entities"]], "Challenges": [[1192, "challenges"]], "OMO": [[1192, "omo"]], "Ontology portals": [[1192, "ontology-portals"]], "OAK Approach": [[1192, "oak-approach"]], "Labels": [[1192, "labels"]], "Obsoletion and obsoletion metadata": [[1192, "obsoletion-and-obsoletion-metadata"]], "Search Syntax": [[1193, "search-syntax"]], "Boolean Combinations": [[1193, "boolean-combinations"]], "Search Datamodel": [[1193, "search-datamodel"]]}, "indexentries": {"--about": [[0, "cmdoption-runoak-axioms-about"]], "--adapter-mapping": [[0, "cmdoption-runoak-validate-mappings-adapter-mapping"]], "--add": [[0, "cmdoption-runoak-a"]], "--add-closure-fields": [[0, "cmdoption-runoak-associations-add-closure-fields"]], "--add-labels": [[0, "cmdoption-runoak-lexmatch-add-labels"]], "--add-mrcas": [[0, "cmdoption-runoak-tree-add-mrcas"], [0, "cmdoption-runoak-viz-add-mrcas"]], "--additional-metadata": [[0, "cmdoption-runoak-definitions-additional-metadata"], [0, "cmdoption-runoak-term-metadata-additional-metadata"]], "--all": [[0, "cmdoption-runoak-ontology-metadata-all"], [0, "cmdoption-runoak-ontology-versions-all"], [0, "cmdoption-runoak-taxon-constraints-A"]], "--all-languages": [[0, "cmdoption-runoak-labels-all-languages"]], "--allow-missing": [[0, "cmdoption-runoak-fill-table-allow-missing"]], "--analyze": [[0, "cmdoption-runoak-generate-logical-definitions-analyze"]], "--annotated-roots": [[0, "cmdoption-runoak-roots-A"]], "--apply-patch": [[0, "cmdoption-runoak-generate-definitions-apply-patch"], [0, "cmdoption-runoak-generate-synonyms-apply-patch"], [0, "cmdoption-runoak-synonymize-apply-patch"]], "--association-predicates": [[0, "cmdoption-runoak-associations-association-predicates"], [0, "cmdoption-runoak-associations-matrix-association-predicates"], [0, "cmdoption-runoak-enrichment-association-predicates"]], "--associations": [[0, "cmdoption-runoak-diff-associations-g"], [0, "cmdoption-runoak-g"]], "--associations-type": [[0, "cmdoption-runoak-G"]], "--autolabel": [[0, "cmdoption-runoak-associations-autolabel"], [0, "cmdoption-runoak-associations-matrix-autolabel"], [0, "cmdoption-runoak-definitions-autolabel"], [0, "cmdoption-runoak-diff-associations-autolabel"], [0, "cmdoption-runoak-diff-via-mappings-autolabel"], [0, "cmdoption-runoak-disjoints-autolabel"], [0, "cmdoption-runoak-enrichment-autolabel"], [0, "cmdoption-runoak-fill-table-autolabel"], [0, "cmdoption-runoak-generate-disjoints-autolabel"], [0, "cmdoption-runoak-generate-logical-definitions-autolabel"], [0, "cmdoption-runoak-logical-definitions-autolabel"], [0, "cmdoption-runoak-mappings-autolabel"], [0, "cmdoption-runoak-normalize-autolabel"], [0, "cmdoption-runoak-paths-autolabel"], [0, "cmdoption-runoak-query-autolabel"], [0, "cmdoption-runoak-relationships-autolabel"], [0, "cmdoption-runoak-rollup-autolabel"], [0, "cmdoption-runoak-search-autolabel"], [0, "cmdoption-runoak-similarity-autolabel"], [0, "cmdoption-runoak-similarity-pair-autolabel"], [0, "cmdoption-runoak-termset-similarity-autolabel"], [0, "cmdoption-runoak-validate-mappings-autolabel"]], "--autosave": [[0, "cmdoption-runoak-autosave"]], "--axiom-type": [[0, "cmdoption-runoak-axioms-axiom-type"]], "--background-file": [[0, "cmdoption-runoak-enrichment-B"]], "--bidirectional": [[0, "cmdoption-runoak-diff-via-mappings-bidirectional"]], "--category-system": [[0, "cmdoption-runoak-term-categories-category-system"]], "--change-type": [[0, "cmdoption-runoak-diff-change-type"]], "--changes-format": [[0, "cmdoption-runoak-apply-changes-format"]], "--changes-input": [[0, "cmdoption-runoak-apply-changes-input"]], "--changes-output": [[0, "cmdoption-runoak-apply-changes-output"]], "--comment": [[0, "cmdoption-runoak-fill-table-comment"]], "--compare-with": [[0, "cmdoption-runoak-statistics-X"]], "--config-file": [[0, "cmdoption-runoak-dump-c"], [0, "cmdoption-runoak-transform-c"]], "--configuration-file": [[0, "cmdoption-runoak-annotate-C"], [0, "cmdoption-runoak-validate-mappings-C"]], "--configure": [[0, "cmdoption-runoak-paths-C"], [0, "cmdoption-runoak-tree-C"], [0, "cmdoption-runoak-viz-C"]], "--contributor": [[0, "cmdoption-runoak-apply-contributor"]], "--cutoff": [[0, "cmdoption-runoak-enrichment-cutoff"], [0, "cmdoption-runoak-validate-cutoff"], [0, "cmdoption-runoak-validate-multiple-cutoff"]], "--dangling": [[0, "cmdoption-runoak-extract-dangling"]], "--days-old": [[0, "cmdoption-runoak-cache-clear-days-old"]], "--delimiter": [[0, "cmdoption-runoak-fill-table-delimiter"]], "--direct": [[0, "cmdoption-runoak-taxon-constraints-direct"]], "--directed": [[0, "cmdoption-runoak-paths-directed"]], "--direction": [[0, "cmdoption-runoak-relationships-direction"]], "--display": [[0, "cmdoption-runoak-definitions-D"], [0, "cmdoption-runoak-descendants-D"], [0, "cmdoption-runoak-info-D"], [0, "cmdoption-runoak-labels-D"], [0, "cmdoption-runoak-tree-D"]], "--down": [[0, "cmdoption-runoak-tree-down"], [0, "cmdoption-runoak-viz-down"]], "--dry-run": [[0, "cmdoption-runoak-apply-dry-run"], [0, "cmdoption-runoak-lint-dry-run"]], "--endpoint": [[0, "cmdoption-runoak-set-apikey-e"]], "--enforce-canonical-ordering": [[0, "cmdoption-runoak-dump-enforce-canonical-ordering"]], "--ensure-strict-prefixes": [[0, "cmdoption-runoak-lexmatch-ensure-strict-prefixes"]], "--evolution-file": [[0, "cmdoption-runoak-apply-taxon-constraints-E"]], "--exclude-existing": [[0, "cmdoption-runoak-generate-disjoints-exclude-existing"]], "--exclude-predicates": [[0, "cmdoption-runoak-paths-exclude-predicates"]], "--exclude-tokens": [[0, "cmdoption-runoak-annotate-x"]], "--expand": [[0, "cmdoption-runoak-apply-expand"], [0, "cmdoption-runoak-apply-obsolete-expand"]], "--fill": [[0, "cmdoption-runoak-generate-logical-definitions-fill"]], "--filter-category-identical": [[0, "cmdoption-runoak-diff-via-mappings-filter-category-identical"]], "--filter-obsoletes": [[0, "cmdoption-runoak-leafs-filter-obsoletes"], [0, "cmdoption-runoak-singletons-filter-obsoletes"], [0, "cmdoption-runoak-terms-filter-obsoletes"]], "--filter-redundant": [[0, "cmdoption-runoak-enrichment-filter-redundant"]], "--gap-fill": [[0, "cmdoption-runoak-tree-gap-fill"], [0, "cmdoption-runoak-viz-gap-fill"]], "--graph-traversal-method": [[0, "cmdoption-runoak-ancestors-M"], [0, "cmdoption-runoak-apply-taxon-constraints-M"], [0, "cmdoption-runoak-descendants-M"], [0, "cmdoption-runoak-taxon-constraints-M"]], "--group-by": [[0, "cmdoption-runoak-diff-associations-group-by"]], "--group-by-defined-by": [[0, "cmdoption-runoak-diff-group-by-defined-by"], [0, "cmdoption-runoak-statistics-group-by-defined-by"]], "--group-by-obo-namespace": [[0, "cmdoption-runoak-diff-group-by-obo-namespace"], [0, "cmdoption-runoak-statistics-group-by-obo-namespace"]], "--group-by-prefix": [[0, "cmdoption-runoak-diff-group-by-prefix"], [0, "cmdoption-runoak-statistics-group-by-prefix"]], "--group-by-property": [[0, "cmdoption-runoak-diff-group-by-property"], [0, "cmdoption-runoak-statistics-group-by-property"]], "--has-prefix": [[0, "cmdoption-runoak-roots-P"], [0, "cmdoption-runoak-statistics-P"]], "--if-absent": [[0, "cmdoption-runoak-associations-if-absent"], [0, "cmdoption-runoak-definitions-if-absent"], [0, "cmdoption-runoak-labels-if-absent"], [0, "cmdoption-runoak-logical-definitions-if-absent"], [0, "cmdoption-runoak-relationships-if-absent"]], "--ignore-invalid-changes": [[0, "cmdoption-runoak-apply-ignore-invalid-changes"], [0, "cmdoption-runoak-apply-obsolete-ignore-invalid-changes"]], "--import-depth": [[0, "cmdoption-runoak-import-depth"]], "--include-abox": [[0, "cmdoption-runoak-relationships-include-abox"]], "--include-aliases": [[0, "cmdoption-runoak-annotate-include-aliases"]], "--include-entailed": [[0, "cmdoption-runoak-relationships-include-entailed"]], "--include-identity-mappings": [[0, "cmdoption-runoak-diff-via-mappings-include-identity-mappings"]], "--include-merged": [[0, "cmdoption-runoak-obsoletes-include-merged"]], "--include-metadata": [[0, "cmdoption-runoak-extract-include-metadata"], [0, "cmdoption-runoak-relationships-include-metadata"]], "--include-predicates": [[0, "cmdoption-runoak-paths-include-predicates"]], "--include-redundant": [[0, "cmdoption-runoak-taxon-constraints-include-redundant"]], "--include-residuals": [[0, "cmdoption-runoak-statistics-include-residuals"]], "--include-tbox": [[0, "cmdoption-runoak-relationships-include-tbox"]], "--information-content-file": [[0, "cmdoption-runoak-similarity-information-content-file"], [0, "cmdoption-runoak-termset-similarity-information-content-file"]], "--input": [[0, "cmdoption-runoak-i"]], "--input-type": [[0, "cmdoption-runoak-I"]], "--intra": [[0, "cmdoption-runoak-diff-via-mappings-intra"]], "--label-fields": [[0, "cmdoption-runoak-query-L"]], "--lexical-index-file": [[0, "cmdoption-runoak-annotate-L"], [0, "cmdoption-runoak-lexmatch-L"]], "--main-score-field": [[0, "cmdoption-runoak-similarity-main-score-field"]], "--mapper": [[0, "cmdoption-runoak-mappings-mapper"]], "--mapping-input": [[0, "cmdoption-runoak-diff-via-mappings-mapping-input"]], "--maps-to-source": [[0, "cmdoption-runoak-mappings-M"], [0, "cmdoption-runoak-normalize-M"]], "--match-column": [[0, "cmdoption-runoak-annotate-A"]], "--matches-whole-text": [[0, "cmdoption-runoak-annotate-W"]], "--matrix-axes": [[0, "cmdoption-runoak-logical-definitions-matrix-axes"]], "--max-hops": [[0, "cmdoption-runoak-tree-max-hops"], [0, "cmdoption-runoak-viz-max-hops"]], "--merge": [[0, "cmdoption-runoak-merge"]], "--meta": [[0, "cmdoption-runoak-viz-meta"]], "--metamodel-mappings": [[0, "cmdoption-runoak-metamodel-mappings"]], "--min-ancestor-information-content": [[0, "cmdoption-runoak-similarity-min-ancestor-information-content"]], "--min-descendants": [[0, "cmdoption-runoak-generate-disjoints-M"]], "--min-jaccard-similarity": [[0, "cmdoption-runoak-similarity-min-jaccard-similarity"]], "--missing-value-token": [[0, "cmdoption-runoak-fill-table-missing-value-token"]], "--model": [[0, "cmdoption-runoak-annotate-m"]], "--named-classes-only": [[0, "cmdoption-runoak-disjoints-named-classes-only"]], "--named-prefix-map": [[0, "cmdoption-runoak-named-prefix-map"]], "--narrow": [[0, "cmdoption-runoak-paths-narrow"]], "--new-date": [[0, "cmdoption-runoak-diff-associations-new-date"]], "--no-a": [[0, "cmdoption-runoak-roots-A"], [0, "cmdoption-runoak-taxon-constraints-A"]], "--no-w": [[0, "cmdoption-runoak-annotate-W"]], "--no-add-closure-fields": [[0, "cmdoption-runoak-associations-add-closure-fields"]], "--no-add-labels": [[0, "cmdoption-runoak-lexmatch-add-labels"]], "--no-add-mrcas": [[0, "cmdoption-runoak-tree-add-mrcas"], [0, "cmdoption-runoak-viz-add-mrcas"]], "--no-additional-metadata": [[0, "cmdoption-runoak-definitions-additional-metadata"], [0, "cmdoption-runoak-term-metadata-additional-metadata"]], "--no-all": [[0, "cmdoption-runoak-ontology-metadata-all"], [0, "cmdoption-runoak-ontology-versions-all"], [0, "cmdoption-runoak-taxon-constraints-A"]], "--no-all-languages": [[0, "cmdoption-runoak-labels-all-languages"]], "--no-allow-missing": [[0, "cmdoption-runoak-fill-table-allow-missing"]], "--no-analyze": [[0, "cmdoption-runoak-generate-logical-definitions-analyze"]], "--no-annotated-roots": [[0, "cmdoption-runoak-roots-A"]], "--no-apply-patch": [[0, "cmdoption-runoak-generate-definitions-apply-patch"], [0, "cmdoption-runoak-generate-synonyms-apply-patch"], [0, "cmdoption-runoak-synonymize-apply-patch"]], "--no-autolabel": [[0, "cmdoption-runoak-associations-autolabel"], [0, "cmdoption-runoak-associations-matrix-autolabel"], [0, "cmdoption-runoak-definitions-autolabel"], [0, "cmdoption-runoak-diff-associations-autolabel"], [0, "cmdoption-runoak-diff-via-mappings-autolabel"], [0, "cmdoption-runoak-disjoints-autolabel"], [0, "cmdoption-runoak-enrichment-autolabel"], [0, "cmdoption-runoak-fill-table-autolabel"], [0, "cmdoption-runoak-generate-disjoints-autolabel"], [0, "cmdoption-runoak-generate-logical-definitions-autolabel"], [0, "cmdoption-runoak-logical-definitions-autolabel"], [0, "cmdoption-runoak-mappings-autolabel"], [0, "cmdoption-runoak-normalize-autolabel"], [0, "cmdoption-runoak-paths-autolabel"], [0, "cmdoption-runoak-query-autolabel"], [0, "cmdoption-runoak-relationships-autolabel"], [0, "cmdoption-runoak-rollup-autolabel"], [0, "cmdoption-runoak-search-autolabel"], [0, "cmdoption-runoak-similarity-autolabel"], [0, "cmdoption-runoak-similarity-pair-autolabel"], [0, "cmdoption-runoak-termset-similarity-autolabel"], [0, "cmdoption-runoak-validate-mappings-autolabel"]], "--no-autosave": [[0, "cmdoption-runoak-autosave"]], "--no-bidirectional": [[0, "cmdoption-runoak-diff-via-mappings-bidirectional"]], "--no-dangling": [[0, "cmdoption-runoak-extract-dangling"]], "--no-direct": [[0, "cmdoption-runoak-taxon-constraints-direct"]], "--no-directed": [[0, "cmdoption-runoak-paths-directed"]], "--no-down": [[0, "cmdoption-runoak-tree-down"], [0, "cmdoption-runoak-viz-down"]], "--no-dry-run": [[0, "cmdoption-runoak-apply-dry-run"], [0, "cmdoption-runoak-lint-dry-run"]], "--no-enforce-canonical-ordering": [[0, "cmdoption-runoak-dump-enforce-canonical-ordering"]], "--no-ensure-strict-prefixes": [[0, "cmdoption-runoak-lexmatch-ensure-strict-prefixes"]], "--no-exclude-existing": [[0, "cmdoption-runoak-generate-disjoints-exclude-existing"]], "--no-expand": [[0, "cmdoption-runoak-apply-expand"], [0, "cmdoption-runoak-apply-obsolete-expand"]], "--no-fill": [[0, "cmdoption-runoak-generate-logical-definitions-fill"]], "--no-filter-category-identical": [[0, "cmdoption-runoak-diff-via-mappings-filter-category-identical"]], "--no-filter-obsoletes": [[0, "cmdoption-runoak-leafs-filter-obsoletes"], [0, "cmdoption-runoak-singletons-filter-obsoletes"], [0, "cmdoption-runoak-terms-filter-obsoletes"]], "--no-filter-redundant": [[0, "cmdoption-runoak-enrichment-filter-redundant"]], "--no-gap-fill": [[0, "cmdoption-runoak-tree-gap-fill"], [0, "cmdoption-runoak-viz-gap-fill"]], "--no-group-by-defined-by": [[0, "cmdoption-runoak-diff-group-by-defined-by"], [0, "cmdoption-runoak-statistics-group-by-defined-by"]], "--no-group-by-obo-namespace": [[0, "cmdoption-runoak-diff-group-by-obo-namespace"], [0, "cmdoption-runoak-statistics-group-by-obo-namespace"]], "--no-group-by-prefix": [[0, "cmdoption-runoak-diff-group-by-prefix"], [0, "cmdoption-runoak-statistics-group-by-prefix"]], "--no-ignore-invalid-changes": [[0, "cmdoption-runoak-apply-ignore-invalid-changes"], [0, "cmdoption-runoak-apply-obsolete-ignore-invalid-changes"]], "--no-include-abox": [[0, "cmdoption-runoak-relationships-include-abox"]], "--no-include-aliases": [[0, "cmdoption-runoak-annotate-include-aliases"]], "--no-include-entailed": [[0, "cmdoption-runoak-relationships-include-entailed"]], "--no-include-identity-mappings": [[0, "cmdoption-runoak-diff-via-mappings-include-identity-mappings"]], "--no-include-merged": [[0, "cmdoption-runoak-obsoletes-include-merged"]], "--no-include-metadata": [[0, "cmdoption-runoak-extract-include-metadata"], [0, "cmdoption-runoak-relationships-include-metadata"]], "--no-include-predicates": [[0, "cmdoption-runoak-paths-include-predicates"]], "--no-include-redundant": [[0, "cmdoption-runoak-taxon-constraints-include-redundant"]], "--no-include-residuals": [[0, "cmdoption-runoak-statistics-include-residuals"]], "--no-include-tbox": [[0, "cmdoption-runoak-relationships-include-tbox"]], "--no-intra": [[0, "cmdoption-runoak-diff-via-mappings-intra"]], "--no-matches-whole-text": [[0, "cmdoption-runoak-annotate-W"]], "--no-merge": [[0, "cmdoption-runoak-merge"]], "--no-meta": [[0, "cmdoption-runoak-viz-meta"]], "--no-named-classes-only": [[0, "cmdoption-runoak-disjoints-named-classes-only"]], "--no-narrow": [[0, "cmdoption-runoak-paths-narrow"]], "--no-obo-model": [[0, "cmdoption-runoak-aliases-obo-model"]], "--no-ontology-only": [[0, "cmdoption-runoak-enrichment-ontology-only"]], "--no-overwrite": [[0, "cmdoption-runoak-apply-overwrite"]], "--no-parse": [[0, "cmdoption-runoak-generate-logical-definitions-parse"]], "--no-pivot-languages": [[0, "cmdoption-runoak-labels-pivot-languages"]], "--no-quiet": [[0, "cmdoption-runoak-q"]], "--no-recreate": [[0, "cmdoption-runoak-lexmatch-recreate"]], "--no-replace": [[0, "cmdoption-runoak-migrate-curies-replace"]], "--no-show-extract": [[0, "cmdoption-runoak-generate-logical-definitions-show-extract"]], "--no-show-migration-relationships": [[0, "cmdoption-runoak-obsoletes-show-migration-relationships"]], "--no-simple": [[0, "cmdoption-runoak-diff-simple"]], "--no-skip-ontology-rules": [[0, "cmdoption-runoak-validate-skip-ontology-rules"]], "--no-skip-structural-validation": [[0, "cmdoption-runoak-validate-skip-structural-validation"]], "--no-skip-text-annotation": [[0, "cmdoption-runoak-validate-definitions-skip-text-annotation"]], "--no-stacktrace": [[0, "cmdoption-runoak-stacktrace"]], "--no-statistics": [[0, "cmdoption-runoak-ancestors-statistics"], [0, "cmdoption-runoak-diff-statistics"]], "--no-unmelt": [[0, "cmdoption-runoak-generate-logical-definitions-unmelt"], [0, "cmdoption-runoak-logical-definitions-unmelt"]], "--no-use-associations": [[0, "cmdoption-runoak-information-content-use-associations"]], "--no-used-only": [[0, "cmdoption-runoak-prefixes-used-only"]], "--no-view": [[0, "cmdoption-runoak-viz-view"]], "--no-viz": [[0, "cmdoption-runoak-paths-viz"]], "--object-group": [[0, "cmdoption-runoak-rollup-object-group"]], "--obo-model": [[0, "cmdoption-runoak-aliases-obo-model"]], "--old-date": [[0, "cmdoption-runoak-diff-associations-old-date"]], "--ontology-only": [[0, 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"datamodels/association/AssociationChange", "datamodels/association/Boolean", "datamodels/association/Curie", "datamodels/association/Date", "datamodels/association/DateOrDatetime", "datamodels/association/Datetime", "datamodels/association/Decimal", "datamodels/association/Double", "datamodels/association/Float", "datamodels/association/Integer", "datamodels/association/Jsonpath", "datamodels/association/Jsonpointer", "datamodels/association/Ncname", "datamodels/association/NegatedAssociation", "datamodels/association/Nodeidentifier", "datamodels/association/Objectidentifier", "datamodels/association/PairwiseCoAssociation", "datamodels/association/ParserConfiguration", "datamodels/association/PositiveOrNegativeAssociation", "datamodels/association/PropertyValue", "datamodels/association/RollupGroup", "datamodels/association/Sparqlpath", "datamodels/association/String", "datamodels/association/Time", "datamodels/association/Uri", "datamodels/association/Uriorcurie", "datamodels/association/aggregator_knowledge_source", "datamodels/association/association", "datamodels/association/associations", "datamodels/association/associations_for_subjects_in_common", "datamodels/association/closure_delta", "datamodels/association/closure_information_content_delta", "datamodels/association/closure_predicates", "datamodels/association/comments", "datamodels/association/core_triple", "datamodels/association/creation_date", "datamodels/association/date", "datamodels/association/denormalized_slot", "datamodels/association/diff_slot", "datamodels/association/evidence_type", "datamodels/association/group_object", "datamodels/association/include_association_attributes", "datamodels/association/index", "datamodels/association/is_creation", "datamodels/association/is_deletion", "datamodels/association/is_generalization", "datamodels/association/is_migration", "datamodels/association/is_specialization", "datamodels/association/modification_date", "datamodels/association/negated", "datamodels/association/new_date", "datamodels/association/new_object", "datamodels/association/new_predicate", "datamodels/association/number_subject_unique_to_entity1", "datamodels/association/number_subject_unique_to_entity2", "datamodels/association/number_subjects_in_common", "datamodels/association/object", "datamodels/association/object1", "datamodels/association/object1_label", "datamodels/association/object2", "datamodels/association/object2_label", "datamodels/association/object_closure", "datamodels/association/object_closure_label", "datamodels/association/object_label", "datamodels/association/old_date", "datamodels/association/old_object", "datamodels/association/old_object_obsolete", "datamodels/association/old_predicate", "datamodels/association/original_object", "datamodels/association/original_predicate", "datamodels/association/original_subject", "datamodels/association/predicate", "datamodels/association/predicate_label", "datamodels/association/preserve_negated_associations", "datamodels/association/primary_knowledge_source", "datamodels/association/property_values", "datamodels/association/publication_is_added", "datamodels/association/publication_is_deleted", "datamodels/association/publications", "datamodels/association/sub_groups", "datamodels/association/subject", "datamodels/association/subject_closure", "datamodels/association/subject_closure_label", "datamodels/association/subject_label", "datamodels/association/subjects_in_common", "datamodels/association/summary_group", "datamodels/association/supporting_objects", "datamodels/class-enrichment/Boolean", "datamodels/class-enrichment/ClassEnrichmentConfiguration", "datamodels/class-enrichment/ClassEnrichmentResult", "datamodels/class-enrichment/ClassEnrichmentResultSet", "datamodels/class-enrichment/Curie", "datamodels/class-enrichment/Date", "datamodels/class-enrichment/DateOrDatetime", "datamodels/class-enrichment/Datetime", "datamodels/class-enrichment/Decimal", "datamodels/class-enrichment/Double", "datamodels/class-enrichment/Float", "datamodels/class-enrichment/Integer", "datamodels/class-enrichment/Jsonpath", "datamodels/class-enrichment/Jsonpointer", "datamodels/class-enrichment/Ncname", "datamodels/class-enrichment/Nodeidentifier", "datamodels/class-enrichment/Objectidentifier", "datamodels/class-enrichment/Position", "datamodels/class-enrichment/SortFieldEnum", "datamodels/class-enrichment/Sparqlpath", "datamodels/class-enrichment/String", "datamodels/class-enrichment/Time", "datamodels/class-enrichment/Uri", "datamodels/class-enrichment/Uriorcurie", "datamodels/class-enrichment/ancestor_of_more_informative_result", "datamodels/class-enrichment/background_count", "datamodels/class-enrichment/background_total", "datamodels/class-enrichment/class-enrichment", "datamodels/class-enrichment/class_id", "datamodels/class-enrichment/class_label", "datamodels/class-enrichment/descendant_of_more_informative_result", "datamodels/class-enrichment/direction", "datamodels/class-enrichment/false_discovery_rate", "datamodels/class-enrichment/fold_enrichment", "datamodels/class-enrichment/index", "datamodels/class-enrichment/p_value", "datamodels/class-enrichment/p_value_adjusted", "datamodels/class-enrichment/p_value_cutoff", "datamodels/class-enrichment/probability", "datamodels/class-enrichment/rank", "datamodels/class-enrichment/results", "datamodels/class-enrichment/sample_count", "datamodels/class-enrichment/sample_total", "datamodels/cross-ontology-diff/Boolean", "datamodels/cross-ontology-diff/Curie", "datamodels/cross-ontology-diff/Date", "datamodels/cross-ontology-diff/DateOrDatetime", "datamodels/cross-ontology-diff/Datetime", "datamodels/cross-ontology-diff/Decimal", "datamodels/cross-ontology-diff/DiffCategory", "datamodels/cross-ontology-diff/Double", "datamodels/cross-ontology-diff/EntityReference", "datamodels/cross-ontology-diff/Float", "datamodels/cross-ontology-diff/Integer", "datamodels/cross-ontology-diff/Jsonpath", "datamodels/cross-ontology-diff/Jsonpointer", "datamodels/cross-ontology-diff/Label", "datamodels/cross-ontology-diff/MappingCardinalityEnum", "datamodels/cross-ontology-diff/Ncname", "datamodels/cross-ontology-diff/Nodeidentifier", "datamodels/cross-ontology-diff/Objectidentifier", "datamodels/cross-ontology-diff/Position", "datamodels/cross-ontology-diff/RelationalDiff", "datamodels/cross-ontology-diff/Source", "datamodels/cross-ontology-diff/Sparqlpath", "datamodels/cross-ontology-diff/String", "datamodels/cross-ontology-diff/StructureDiffResultSet", "datamodels/cross-ontology-diff/Time", "datamodels/cross-ontology-diff/Uri", "datamodels/cross-ontology-diff/Uriorcurie", "datamodels/cross-ontology-diff/category", "datamodels/cross-ontology-diff/cross-ontology-diff", "datamodels/cross-ontology-diff/index", "datamodels/cross-ontology-diff/is_functional", "datamodels/cross-ontology-diff/label", "datamodels/cross-ontology-diff/left_object_id", "datamodels/cross-ontology-diff/left_object_is_functional", "datamodels/cross-ontology-diff/left_object_label", "datamodels/cross-ontology-diff/left_object_name", "datamodels/cross-ontology-diff/left_predicate_id", "datamodels/cross-ontology-diff/left_predicate_label", "datamodels/cross-ontology-diff/left_predicate_name", "datamodels/cross-ontology-diff/left_side", "datamodels/cross-ontology-diff/left_source", "datamodels/cross-ontology-diff/left_subject_id", "datamodels/cross-ontology-diff/left_subject_is_functional", "datamodels/cross-ontology-diff/left_subject_label", "datamodels/cross-ontology-diff/left_subject_name", "datamodels/cross-ontology-diff/object", "datamodels/cross-ontology-diff/object_mapping_cardinality", "datamodels/cross-ontology-diff/object_mapping_predicate", "datamodels/cross-ontology-diff/predicate", "datamodels/cross-ontology-diff/results", "datamodels/cross-ontology-diff/right_intermediate_ids", "datamodels/cross-ontology-diff/right_object_id", "datamodels/cross-ontology-diff/right_object_label", "datamodels/cross-ontology-diff/right_object_name", "datamodels/cross-ontology-diff/right_predicate_ids", "datamodels/cross-ontology-diff/right_predicate_labels", "datamodels/cross-ontology-diff/right_predicate_names", "datamodels/cross-ontology-diff/right_side", "datamodels/cross-ontology-diff/right_source", "datamodels/cross-ontology-diff/right_subject_id", "datamodels/cross-ontology-diff/right_subject_label", "datamodels/cross-ontology-diff/right_subject_name", "datamodels/cross-ontology-diff/side", "datamodels/cross-ontology-diff/subject", "datamodels/cross-ontology-diff/subject_mapping_cardinality", "datamodels/cross-ontology-diff/subject_mapping_predicate", "datamodels/cross-ontology-diff/types", "datamodels/funowl/index", "datamodels/index", "datamodels/item-list/Boolean", "datamodels/item-list/Curie", "datamodels/item-list/Date", "datamodels/item-list/DateOrDatetime", "datamodels/item-list/Datetime", "datamodels/item-list/Decimal", "datamodels/item-list/Double", "datamodels/item-list/Float", "datamodels/item-list/Integer", "datamodels/item-list/ItemList", "datamodels/item-list/ItemListCollection", "datamodels/item-list/ItemListOrderType", "datamodels/item-list/Jsonpath", "datamodels/item-list/Jsonpointer", "datamodels/item-list/ListItem", "datamodels/item-list/Ncname", "datamodels/item-list/Nodeidentifier", "datamodels/item-list/Objectidentifier", "datamodels/item-list/Sparqlpath", "datamodels/item-list/String", "datamodels/item-list/Thing", "datamodels/item-list/Time", "datamodels/item-list/Uri", "datamodels/item-list/Uriorcurie", "datamodels/item-list/additionalType", "datamodels/item-list/categories", "datamodels/item-list/description", "datamodels/item-list/elementId", "datamodels/item-list/id", "datamodels/item-list/idType", "datamodels/item-list/identifiers", "datamodels/item-list/index", "datamodels/item-list/item", "datamodels/item-list/itemList", "datamodels/item-list/itemListElements", "datamodels/item-list/itemLists", "datamodels/item-list/itemMetadataMap", "datamodels/item-list/keywords", "datamodels/item-list/name", "datamodels/item-list/numberOfItems", "datamodels/item-list/position", "datamodels/item-list/previousItem", "datamodels/item-list/type", "datamodels/item-list/url", "datamodels/item-list/wasGeneratedBy", "datamodels/kgcl/index", "datamodels/lexical-index/Activity", "datamodels/lexical-index/Any", "datamodels/lexical-index/Boolean", "datamodels/lexical-index/Curie", "datamodels/lexical-index/Date", "datamodels/lexical-index/DateOrDatetime", "datamodels/lexical-index/Datetime", "datamodels/lexical-index/Decimal", "datamodels/lexical-index/Double", "datamodels/lexical-index/Float", "datamodels/lexical-index/Integer", "datamodels/lexical-index/Jsonpath", "datamodels/lexical-index/Jsonpointer", "datamodels/lexical-index/LexicalGrouping", "datamodels/lexical-index/LexicalIndex", "datamodels/lexical-index/LexicalTransformation", "datamodels/lexical-index/LexicalTransformationPipeline", "datamodels/lexical-index/Ncname", "datamodels/lexical-index/Nodeidentifier", "datamodels/lexical-index/Objectidentifier", "datamodels/lexical-index/RelationshipToTerm", "datamodels/lexical-index/Sparqlpath", "datamodels/lexical-index/String", "datamodels/lexical-index/Time", "datamodels/lexical-index/TransformationType", "datamodels/lexical-index/Uri", "datamodels/lexical-index/Uriorcurie", "datamodels/lexical-index/element", "datamodels/lexical-index/element_term", "datamodels/lexical-index/groupings", "datamodels/lexical-index/index", "datamodels/lexical-index/lexical-index", "datamodels/lexical-index/lexican-index", "datamodels/lexical-index/name", "datamodels/lexical-index/params", "datamodels/lexical-index/pipeline", "datamodels/lexical-index/pipelines", "datamodels/lexical-index/predicate", "datamodels/lexical-index/relationships", "datamodels/lexical-index/source", "datamodels/lexical-index/synonymized", "datamodels/lexical-index/term", "datamodels/lexical-index/transformations", "datamodels/lexical-index/type", "datamodels/lexical-index/types", "datamodels/mapping-rules/Activity", "datamodels/mapping-rules/Any", "datamodels/mapping-rules/Boolean", "datamodels/mapping-rules/Curie", "datamodels/mapping-rules/Date", "datamodels/mapping-rules/DateOrDatetime", "datamodels/mapping-rules/Datetime", "datamodels/mapping-rules/Decimal", "datamodels/mapping-rules/Double", "datamodels/mapping-rules/Float", "datamodels/mapping-rules/Integer", "datamodels/mapping-rules/Jsonpath", "datamodels/mapping-rules/Jsonpointer", "datamodels/mapping-rules/LexicalGrouping", "datamodels/mapping-rules/LexicalIndex", "datamodels/mapping-rules/LexicalTransformation", "datamodels/mapping-rules/LexicalTransformationPipeline", "datamodels/mapping-rules/MappingRule", "datamodels/mapping-rules/MappingRuleCollection", "datamodels/mapping-rules/Ncname", "datamodels/mapping-rules/Nodeidentifier", "datamodels/mapping-rules/Objectidentifier", "datamodels/mapping-rules/Postcondition", "datamodels/mapping-rules/Precondition", "datamodels/mapping-rules/RelationshipToTerm", "datamodels/mapping-rules/Sparqlpath", "datamodels/mapping-rules/String", "datamodels/mapping-rules/Synonymizer", "datamodels/mapping-rules/Test", "datamodels/mapping-rules/Time", "datamodels/mapping-rules/TransformationType", "datamodels/mapping-rules/Uri", "datamodels/mapping-rules/Uriorcurie", "datamodels/mapping-rules/description", "datamodels/mapping-rules/element", "datamodels/mapping-rules/element_term", "datamodels/mapping-rules/groupings", "datamodels/mapping-rules/index", "datamodels/mapping-rules/input", "datamodels/mapping-rules/lexical-index", "datamodels/mapping-rules/lexican-index", "datamodels/mapping-rules/mapping-rules", "datamodels/mapping-rules/mapping-rules-datamodel", "datamodels/mapping-rules/mapping_source_one_of", "datamodels/mapping-rules/match", "datamodels/mapping-rules/match_scope", "datamodels/mapping-rules/minimum_confidence", "datamodels/mapping-rules/name", "datamodels/mapping-rules/object_match_field_one_of", "datamodels/mapping-rules/object_source_one_of", "datamodels/mapping-rules/oneway", "datamodels/mapping-rules/output", "datamodels/mapping-rules/params", "datamodels/mapping-rules/pipeline", "datamodels/mapping-rules/pipelines", "datamodels/mapping-rules/postconditions", "datamodels/mapping-rules/preconditions", "datamodels/mapping-rules/predicate", "datamodels/mapping-rules/predicate_id", "datamodels/mapping-rules/predicate_id_one_of", "datamodels/mapping-rules/prefix", "datamodels/mapping-rules/qualifier", "datamodels/mapping-rules/relationships", "datamodels/mapping-rules/replacement", "datamodels/mapping-rules/rules", "datamodels/mapping-rules/source", "datamodels/mapping-rules/subject_match_field_one_of", "datamodels/mapping-rules/subject_source_one_of", "datamodels/mapping-rules/synonymized", "datamodels/mapping-rules/synonymizer", "datamodels/mapping-rules/term", "datamodels/mapping-rules/tests", "datamodels/mapping-rules/the_rule", "datamodels/mapping-rules/transformations", "datamodels/mapping-rules/transformations_included_in", "datamodels/mapping-rules/type", "datamodels/mapping-rules/types", "datamodels/mapping-rules/weight", "datamodels/obograph/Axiom", "datamodels/obograph/BasicPropertyValue", "datamodels/obograph/Boolean", "datamodels/obograph/Curie", "datamodels/obograph/Date", "datamodels/obograph/DateOrDatetime", "datamodels/obograph/Datetime", "datamodels/obograph/Decimal", "datamodels/obograph/DefinitionPropertyValue", "datamodels/obograph/DisjointClassExpressionsAxiom", "datamodels/obograph/DomainRangeAxiom", "datamodels/obograph/Double", "datamodels/obograph/Edge", "datamodels/obograph/EquivalentNodesSet", "datamodels/obograph/ExistentialRestrictionExpression", "datamodels/obograph/Float", "datamodels/obograph/Graph", "datamodels/obograph/GraphDocument", "datamodels/obograph/Integer", "datamodels/obograph/Jsonpath", "datamodels/obograph/Jsonpointer", "datamodels/obograph/LogicalDefinitionAxiom", "datamodels/obograph/Meta", "datamodels/obograph/Ncname", "datamodels/obograph/Node", "datamodels/obograph/NodeTypeEnum", "datamodels/obograph/Nodeidentifier", "datamodels/obograph/Objectidentifier", "datamodels/obograph/OboIdentifierString", "datamodels/obograph/PredsEnum", "datamodels/obograph/PrefixDeclaration", "datamodels/obograph/PropertyChainAxiom", "datamodels/obograph/PropertyTypeEnum", "datamodels/obograph/PropertyValue", "datamodels/obograph/ScopeEnum", "datamodels/obograph/ScopesEnum", "datamodels/obograph/Sparqlpath", "datamodels/obograph/String", "datamodels/obograph/SubsetDefinition", "datamodels/obograph/SynonymPropertyValue", "datamodels/obograph/SynonymTypeDefinition", "datamodels/obograph/SynonymTypeIdentifierString", "datamodels/obograph/Time", "datamodels/obograph/Uri", "datamodels/obograph/Uriorcurie", "datamodels/obograph/XrefPropertyValue", "datamodels/obograph/XrefString", "datamodels/obograph/allValuesFromEdges", "datamodels/obograph/basicPropertyValues", "datamodels/obograph/chainPredicateIds", "datamodels/obograph/classExpressions", "datamodels/obograph/classIds", "datamodels/obograph/comments", "datamodels/obograph/definedClassId", "datamodels/obograph/definition", "datamodels/obograph/deprecated", "datamodels/obograph/disjointClassExpressionsAxioms", "datamodels/obograph/domainClassIds", "datamodels/obograph/domainRangeAxioms", "datamodels/obograph/edges", "datamodels/obograph/equivalentNodesSets", "datamodels/obograph/fillerId", "datamodels/obograph/genusIds", "datamodels/obograph/graphs", "datamodels/obograph/id", "datamodels/obograph/index", "datamodels/obograph/isExact", "datamodels/obograph/label", "datamodels/obograph/lang", "datamodels/obograph/lbl", "datamodels/obograph/logicalDefinitionAxioms", "datamodels/obograph/meta", "datamodels/obograph/namespace", "datamodels/obograph/nodeIds", "datamodels/obograph/nodes", "datamodels/obograph/obj", "datamodels/obograph/obographs_datamodel", "datamodels/obograph/obographs_linkml_model", "datamodels/obograph/pred", "datamodels/obograph/predicateId", "datamodels/obograph/prefix", "datamodels/obograph/prefixes", "datamodels/obograph/propertyChainAxioms", "datamodels/obograph/propertyId", "datamodels/obograph/propertyType", "datamodels/obograph/rangeClassIds", "datamodels/obograph/representativeNodeId", "datamodels/obograph/representitiveNodeId", "datamodels/obograph/restrictions", "datamodels/obograph/scope", "datamodels/obograph/sub", "datamodels/obograph/subsetDefinitions", "datamodels/obograph/subsets", "datamodels/obograph/synonymType", "datamodels/obograph/synonymTypeDefinitions", "datamodels/obograph/synonyms", "datamodels/obograph/type", "datamodels/obograph/types", "datamodels/obograph/unionEquivalentTo", "datamodels/obograph/unionEquivalentToExpression", "datamodels/obograph/val", "datamodels/obograph/valType", "datamodels/obograph/version", "datamodels/obograph/xrefs", "datamodels/ontology-metadata/Agent", "datamodels/ontology-metadata/AllotropePermittedProfile", "datamodels/ontology-metadata/AllotropeRequiredProfile", "datamodels/ontology-metadata/Annotation", "datamodels/ontology-metadata/AnnotationProperty", "datamodels/ontology-metadata/AnnotationPropertyMixin", "datamodels/ontology-metadata/Anonymous", "datamodels/ontology-metadata/AnonymousClassExpression", "datamodels/ontology-metadata/Any", "datamodels/ontology-metadata/Axiom", "datamodels/ontology-metadata/Boolean", "datamodels/ontology-metadata/CURIELiteral", "datamodels/ontology-metadata/Class", "datamodels/ontology-metadata/ClassExpression", "datamodels/ontology-metadata/Curie", "datamodels/ontology-metadata/Date", "datamodels/ontology-metadata/DateOrDatetime", "datamodels/ontology-metadata/Datetime", "datamodels/ontology-metadata/Decimal", "datamodels/ontology-metadata/DefinitionConstraintComponent", "datamodels/ontology-metadata/Double", "datamodels/ontology-metadata/Expression", "datamodels/ontology-metadata/Float", "datamodels/ontology-metadata/GoPermittedProfile", "datamodels/ontology-metadata/GoRecommendedProfile", "datamodels/ontology-metadata/GoRequiredProfile", "datamodels/ontology-metadata/HasCategory", "datamodels/ontology-metadata/HasLifeCycle", "datamodels/ontology-metadata/HasMappings", "datamodels/ontology-metadata/HasMinimalMetadata", "datamodels/ontology-metadata/HasProvenance", "datamodels/ontology-metadata/HasSynonyms", "datamodels/ontology-metadata/HasUserInformation", "datamodels/ontology-metadata/HomoSapiens", "datamodels/ontology-metadata/IEDB_alternative_term", "datamodels/ontology-metadata/ISA_alternative_term", "datamodels/ontology-metadata/Image", "datamodels/ontology-metadata/Integer", "datamodels/ontology-metadata/IriType", "datamodels/ontology-metadata/Jsonpath", "datamodels/ontology-metadata/Jsonpointer", "datamodels/ontology-metadata/LabelType", "datamodels/ontology-metadata/NCIT_definition_source", "datamodels/ontology-metadata/NCIT_term_source", "datamodels/ontology-metadata/NCIT_term_type", "datamodels/ontology-metadata/NamedIndividual", "datamodels/ontology-metadata/NamedObject", "datamodels/ontology-metadata/NarrativeText", "datamodels/ontology-metadata/Ncname", "datamodels/ontology-metadata/Nodeidentifier", "datamodels/ontology-metadata/NotObsoleteAspect", "datamodels/ontology-metadata/OBO_foundry_unique_label", "datamodels/ontology-metadata/ObiPermittedProfile", "datamodels/ontology-metadata/ObiRequiredProfile", "datamodels/ontology-metadata/ObjectProperty", "datamodels/ontology-metadata/Objectidentifier", "datamodels/ontology-metadata/ObsoleteAspect", "datamodels/ontology-metadata/Ontology", "datamodels/ontology-metadata/Ontology-Metadata", "datamodels/ontology-metadata/Property", "datamodels/ontology-metadata/PropertyExpression", "datamodels/ontology-metadata/Restriction", "datamodels/ontology-metadata/Sparqlpath", "datamodels/ontology-metadata/String", "datamodels/ontology-metadata/Subset", "datamodels/ontology-metadata/Term", "datamodels/ontology-metadata/Thing", "datamodels/ontology-metadata/TidyString", "datamodels/ontology-metadata/Time", "datamodels/ontology-metadata/TransitiveProperty", "datamodels/ontology-metadata/URLLiteral", "datamodels/ontology-metadata/Uri", "datamodels/ontology-metadata/Uriorcurie", "datamodels/ontology-metadata/allValuesFrom", "datamodels/ontology-metadata/alternative_term", "datamodels/ontology-metadata/annotatedProperty", "datamodels/ontology-metadata/annotatedSource", "datamodels/ontology-metadata/annotatedTarget", "datamodels/ontology-metadata/annotations", "datamodels/ontology-metadata/broadMatch", "datamodels/ontology-metadata/cardinality", "datamodels/ontology-metadata/category", "datamodels/ontology-metadata/changeNote", "datamodels/ontology-metadata/closeMatch", "datamodels/ontology-metadata/comment", "datamodels/ontology-metadata/complementOf", "datamodels/ontology-metadata/conformsTo", "datamodels/ontology-metadata/consider", "datamodels/ontology-metadata/contributor", "datamodels/ontology-metadata/core_property", "datamodels/ontology-metadata/created", "datamodels/ontology-metadata/created_by", "datamodels/ontology-metadata/creation_date", "datamodels/ontology-metadata/creator", "datamodels/ontology-metadata/curator_note", "datamodels/ontology-metadata/database_cross_reference", "datamodels/ontology-metadata/date", "datamodels/ontology-metadata/date_retrieved", "datamodels/ontology-metadata/defaultLanguage", "datamodels/ontology-metadata/definition", "datamodels/ontology-metadata/definition_source", "datamodels/ontology-metadata/depicted_by", "datamodels/ontology-metadata/deprecated", "datamodels/ontology-metadata/disconnected_from", "datamodels/ontology-metadata/disjointWith", "datamodels/ontology-metadata/distinctMembers", "datamodels/ontology-metadata/domain", "datamodels/ontology-metadata/editor_note", "datamodels/ontology-metadata/editor_preferred_term", "datamodels/ontology-metadata/equivalentClass", "datamodels/ontology-metadata/equivalentProperty", "datamodels/ontology-metadata/evidence", "datamodels/ontology-metadata/exactMatch", "datamodels/ontology-metadata/example_of_usage", "datamodels/ontology-metadata/excluded_axiom", "datamodels/ontology-metadata/excluded_from_QC_check", "datamodels/ontology-metadata/excluded_subClassOf", "datamodels/ontology-metadata/excluded_synonym", "datamodels/ontology-metadata/external_ontology", "datamodels/ontology-metadata/hasValue", "datamodels/ontology-metadata/has_alternative_id", "datamodels/ontology-metadata/has_axiom_label", "datamodels/ontology-metadata/has_broad_synonym", "datamodels/ontology-metadata/has_curation_status", "datamodels/ontology-metadata/has_exact_synonym", "datamodels/ontology-metadata/has_narrow_synonym", "datamodels/ontology-metadata/has_obo_namespace", "datamodels/ontology-metadata/has_obsolescence_reason", "datamodels/ontology-metadata/has_ontology_root_term", "datamodels/ontology-metadata/has_rank", "datamodels/ontology-metadata/has_related_synonym", "datamodels/ontology-metadata/has_synonym_type", "datamodels/ontology-metadata/id", "datamodels/ontology-metadata/image", "datamodels/ontology-metadata/imported_from", "datamodels/ontology-metadata/imports", "datamodels/ontology-metadata/in_subset", "datamodels/ontology-metadata/index", "datamodels/ontology-metadata/informative_property", "datamodels/ontology-metadata/intersectionOf", "datamodels/ontology-metadata/inverseOf", "datamodels/ontology-metadata/isDefinedBy", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive", "datamodels/ontology-metadata/is_class_level", "datamodels/ontology-metadata/is_cyclic", "datamodels/ontology-metadata/is_inferred", "datamodels/ontology-metadata/is_metadata_tag", "datamodels/ontology-metadata/is_transitive", "datamodels/ontology-metadata/label", "datamodels/ontology-metadata/language", "datamodels/ontology-metadata/license", "datamodels/ontology-metadata/logical_predicate", "datamodels/ontology-metadata/match", "datamodels/ontology-metadata/match_aspect", "datamodels/ontology-metadata/maxQualifiedCardinality", "datamodels/ontology-metadata/members", "datamodels/ontology-metadata/minCardinality", "datamodels/ontology-metadata/minQualifiedCardinality", "datamodels/ontology-metadata/narrowMatch", "datamodels/ontology-metadata/never_in_taxon", "datamodels/ontology-metadata/notes", "datamodels/ontology-metadata/object", "datamodels/ontology-metadata/oboInOwl_id", "datamodels/ontology-metadata/oboInOwl_ontology", "datamodels/ontology-metadata/obsoletion_related_property", "datamodels/ontology-metadata/omo-schema", "datamodels/ontology-metadata/onClass", "datamodels/ontology-metadata/onProperty", "datamodels/ontology-metadata/oneOf", "datamodels/ontology-metadata/ontology_term_requester", "datamodels/ontology-metadata/page", "datamodels/ontology-metadata/predicate", "datamodels/ontology-metadata/propertyChainAxiom", "datamodels/ontology-metadata/provenance_property", "datamodels/ontology-metadata/qualifiedCardinality", "datamodels/ontology-metadata/range", "datamodels/ontology-metadata/reification_predicate", "datamodels/ontology-metadata/sameAs", "datamodels/ontology-metadata/seeAlso", "datamodels/ontology-metadata/shortcut_annotation_property", "datamodels/ontology-metadata/shorthand", "datamodels/ontology-metadata/should_conform_to", "datamodels/ontology-metadata/someValuesFrom", "datamodels/ontology-metadata/source", "datamodels/ontology-metadata/subClassOf", "datamodels/ontology-metadata/synonym", "datamodels/ontology-metadata/temporal_interpretation", "datamodels/ontology-metadata/term_editor", "datamodels/ontology-metadata/term_replaced_by", "datamodels/ontology-metadata/term_tracker_item", "datamodels/ontology-metadata/title", "datamodels/ontology-metadata/type", "datamodels/ontology-metadata/types", "datamodels/ontology-metadata/unionOf", "datamodels/ontology-metadata/url", "datamodels/ontology-metadata/versionIRI", "datamodels/ontology-metadata/versionInfo", "datamodels/ontology-metadata/version_property", "datamodels/search/Boolean", "datamodels/search/BooleanOperator", "datamodels/search/ComplexQuery", "datamodels/search/Curie", "datamodels/search/Date", "datamodels/search/DateOrDatetime", "datamodels/search/Datetime", "datamodels/search/Decimal", "datamodels/search/Double", "datamodels/search/Float", "datamodels/search/GraphFunction", "datamodels/search/Integer", "datamodels/search/Jsonpath", "datamodels/search/Jsonpointer", "datamodels/search/Ncname", "datamodels/search/Nodeidentifier", "datamodels/search/Objectidentifier", "datamodels/search/PathExpression", "datamodels/search/SearchBaseConfiguration", "datamodels/search/SearchProperty", "datamodels/search/SearchResult", "datamodels/search/SearchResultSet", "datamodels/search/SearchTerm", "datamodels/search/SearchTermSyntax", "datamodels/search/Sparqlpath", "datamodels/search/String", "datamodels/search/Time", "datamodels/search/Uri", "datamodels/search/Uriorcurie", "datamodels/search/all_of", "datamodels/search/any_of", "datamodels/search/atom", "datamodels/search/categories", "datamodels/search/configuration", "datamodels/search/cursor", "datamodels/search/force_case_insensitive", "datamodels/search/graph_predicates", "datamodels/search/include_aliases", "datamodels/search/include_definition", "datamodels/search/include_id", "datamodels/search/include_label", "datamodels/search/include_obsoletes_in_results", "datamodels/search/index", "datamodels/search/is_complete", "datamodels/search/is_fuzzy", "datamodels/search/is_partial", "datamodels/search/is_regular_expression", "datamodels/search/limit", "datamodels/search/matches_full_search_term", "datamodels/search/none_of", "datamodels/search/object_id", "datamodels/search/object_label", "datamodels/search/object_match_field", "datamodels/search/object_source", "datamodels/search/object_source_version", "datamodels/search/path_to", "datamodels/search/properties", "datamodels/search/rank", "datamodels/search/result_count", "datamodels/search/results", "datamodels/search/search-datamodel", "datamodels/search/search_term", "datamodels/search/search_terms", "datamodels/search/snippet", "datamodels/search/syntax", "datamodels/search/traversal", "datamodels/search/types", "datamodels/semsql/index", "datamodels/similarity/BestMatch", "datamodels/similarity/Boolean", "datamodels/similarity/Curie", "datamodels/similarity/Date", "datamodels/similarity/DateOrDatetime", "datamodels/similarity/Datetime", "datamodels/similarity/Decimal", "datamodels/similarity/Double", "datamodels/similarity/Float", "datamodels/similarity/Integer", "datamodels/similarity/ItemCount", "datamodels/similarity/Jsonpath", "datamodels/similarity/Jsonpointer", "datamodels/similarity/Ncname", "datamodels/similarity/NegativeLogValue", "datamodels/similarity/Nodeidentifier", "datamodels/similarity/NonNegativeFloat", "datamodels/similarity/Objectidentifier", "datamodels/similarity/PairwiseSimilarity", "datamodels/similarity/Sparqlpath", "datamodels/similarity/String", "datamodels/similarity/TermInfo", "datamodels/similarity/TermPairwiseSimilarity", "datamodels/similarity/TermSetPairwiseSimilarity", "datamodels/similarity/Time", "datamodels/similarity/Uri", "datamodels/similarity/Uriorcurie", "datamodels/similarity/ZeroToOne", "datamodels/similarity/ancestor_id", "datamodels/similarity/ancestor_information_content", "datamodels/similarity/ancestor_label", "datamodels/similarity/ancestor_source", "datamodels/similarity/average_score", "datamodels/similarity/best_score", "datamodels/similarity/cosine_similarity", "datamodels/similarity/dice_similarity", "datamodels/similarity/id", "datamodels/similarity/index", "datamodels/similarity/information_content", "datamodels/similarity/intersection_count", "datamodels/similarity/jaccard_similarity", "datamodels/similarity/label", "datamodels/similarity/match_source", "datamodels/similarity/match_source_label", "datamodels/similarity/match_subsumer", "datamodels/similarity/match_subsumer_label", "datamodels/similarity/match_target", "datamodels/similarity/match_target_label", "datamodels/similarity/metric", "datamodels/similarity/object_best_matches", "datamodels/similarity/object_id", "datamodels/similarity/object_information_content", "datamodels/similarity/object_label", "datamodels/similarity/object_source", "datamodels/similarity/object_termset", "datamodels/similarity/overlap_coefficient", "datamodels/similarity/phenodigm_score", "datamodels/similarity/score", "datamodels/similarity/similarity", "datamodels/similarity/subject_best_matches", "datamodels/similarity/subject_id", "datamodels/similarity/subject_information_content", "datamodels/similarity/subject_label", "datamodels/similarity/subject_source", "datamodels/similarity/subject_termset", "datamodels/similarity/subsumed_by_score", "datamodels/similarity/subsumes_score", "datamodels/similarity/types", "datamodels/similarity/union_count", "datamodels/sssom/index", "datamodels/summary-statistics/Agent", "datamodels/summary-statistics/Boolean", "datamodels/summary-statistics/ChangeTypeStatistic", "datamodels/summary-statistics/ContributorRole", "datamodels/summary-statistics/ContributorStatistics", "datamodels/summary-statistics/Curie", "datamodels/summary-statistics/Date", "datamodels/summary-statistics/DateOrDatetime", "datamodels/summary-statistics/Datetime", "datamodels/summary-statistics/Decimal", "datamodels/summary-statistics/Double", "datamodels/summary-statistics/FacetStatistics", "datamodels/summary-statistics/FacetedCount", "datamodels/summary-statistics/Float", "datamodels/summary-statistics/GlobalStatistics", "datamodels/summary-statistics/GroupedStatistics", "datamodels/summary-statistics/Integer", "datamodels/summary-statistics/Jsonpath", "datamodels/summary-statistics/Jsonpointer", "datamodels/summary-statistics/Ncname", "datamodels/summary-statistics/Nodeidentifier", "datamodels/summary-statistics/Objectidentifier", "datamodels/summary-statistics/Ontology", "datamodels/summary-statistics/Sparqlpath", "datamodels/summary-statistics/String", "datamodels/summary-statistics/SummaryStatisticCollection", "datamodels/summary-statistics/SummaryStatisticsCalculationActivity", "datamodels/summary-statistics/SummaryStatisticsReport", "datamodels/summary-statistics/Time", "datamodels/summary-statistics/UngroupedStatistics", "datamodels/summary-statistics/Uri", "datamodels/summary-statistics/Uriorcurie", "datamodels/summary-statistics/acted_on_behalf_of", "datamodels/summary-statistics/agents", "datamodels/summary-statistics/annotation_property_count", "datamodels/summary-statistics/anonymous_class_expression_count", "datamodels/summary-statistics/anonymous_individual_count", "datamodels/summary-statistics/by_category", "datamodels/summary-statistics/by_ontology", "datamodels/summary-statistics/by_subset", "datamodels/summary-statistics/by_taxon", "datamodels/summary-statistics/change_summary", "datamodels/summary-statistics/class_count", "datamodels/summary-statistics/class_count_by_category", "datamodels/summary-statistics/class_count_by_subset", "datamodels/summary-statistics/class_count_excluding_deprecated", "datamodels/summary-statistics/class_count_with_definitions", "datamodels/summary-statistics/class_count_with_text_definitions", "datamodels/summary-statistics/class_count_without_text_definitions", "datamodels/summary-statistics/class_statistic_group", "datamodels/summary-statistics/compared_with", "datamodels/summary-statistics/contributor_id", "datamodels/summary-statistics/contributor_name", "datamodels/summary-statistics/contributor_summary", "datamodels/summary-statistics/count_statistic", "datamodels/summary-statistics/datatype_property_count", "datamodels/summary-statistics/deprecated_class_count", "datamodels/summary-statistics/deprecated_object_property_count", "datamodels/summary-statistics/description", "datamodels/summary-statistics/description_logic_profile", "datamodels/summary-statistics/distinct_synonym_count", "datamodels/summary-statistics/edge_count_by_predicate", "datamodels/summary-statistics/ended_at_time", "datamodels/summary-statistics/entailed_edge_count_by_predicate", "datamodels/summary-statistics/equivalent_classes_axiom_count", "datamodels/summary-statistics/equivalentclasses_axiom_count", "datamodels/summary-statistics/facet", "datamodels/summary-statistics/filtered_count", "datamodels/summary-statistics/id", "datamodels/summary-statistics/index", "datamodels/summary-statistics/individual_count", "datamodels/summary-statistics/individual_statistic_group", "datamodels/summary-statistics/label", "datamodels/summary-statistics/mapping_count", "datamodels/summary-statistics/mapping_statement_count_by_object_source", "datamodels/summary-statistics/mapping_statement_count_by_predicate", "datamodels/summary-statistics/mapping_statement_count_subject_by_object_source", "datamodels/summary-statistics/merged_class_count", "datamodels/summary-statistics/metadata_statistic_group", "datamodels/summary-statistics/named_individual_count", "datamodels/summary-statistics/non_deprecated_class_count", "datamodels/summary-statistics/non_deprecated_object_property_count", "datamodels/summary-statistics/normalization_comments", "datamodels/summary-statistics/object_property_count", "datamodels/summary-statistics/ontologies", "datamodels/summary-statistics/ontology_count", "datamodels/summary-statistics/owl_axiom_count", "datamodels/summary-statistics/owl_statistic_group", "datamodels/summary-statistics/partitions", "datamodels/summary-statistics/prefix", "datamodels/summary-statistics/property_count", "datamodels/summary-statistics/property_statistic_group", "datamodels/summary-statistics/rdf_triple_count", "datamodels/summary-statistics/role_counts", "datamodels/summary-statistics/started_at_time", "datamodels/summary-statistics/subclass_of_axiom_count", "datamodels/summary-statistics/subset_count", "datamodels/summary-statistics/summary-statistics", "datamodels/summary-statistics/synonym_statement_count", "datamodels/summary-statistics/synonym_statement_count_by_predicate", "datamodels/summary-statistics/title", "datamodels/summary-statistics/types", "datamodels/summary-statistics/unsatisfiable_class_count", "datamodels/summary-statistics/untyped_entity_count", "datamodels/summary-statistics/version", "datamodels/summary-statistics/version_info", "datamodels/summary-statistics/was_associated_with", "datamodels/summary-statistics/was_generated_by", "datamodels/taxon-constraints/Boolean", "datamodels/taxon-constraints/ConfigurationOption", "datamodels/taxon-constraints/Curie", "datamodels/taxon-constraints/Date", "datamodels/taxon-constraints/DateOrDatetime", "datamodels/taxon-constraints/Datetime", "datamodels/taxon-constraints/Decimal", "datamodels/taxon-constraints/Double", "datamodels/taxon-constraints/Float", "datamodels/taxon-constraints/Integer", "datamodels/taxon-constraints/Jsonpath", "datamodels/taxon-constraints/Jsonpointer", "datamodels/taxon-constraints/Ncname", "datamodels/taxon-constraints/Nodeidentifier", "datamodels/taxon-constraints/Objectidentifier", "datamodels/taxon-constraints/PredicateTerm", "datamodels/taxon-constraints/Sparqlpath", "datamodels/taxon-constraints/String", "datamodels/taxon-constraints/SubjectTerm", "datamodels/taxon-constraints/Taxon", "datamodels/taxon-constraints/TaxonConstraint", "datamodels/taxon-constraints/Term", "datamodels/taxon-constraints/Time", "datamodels/taxon-constraints/Uri", "datamodels/taxon-constraints/Uriorcurie", "datamodels/taxon-constraints/asserted", "datamodels/taxon-constraints/candidate", "datamodels/taxon-constraints/comments", "datamodels/taxon-constraints/contradicted_by", "datamodels/taxon-constraints/description", "datamodels/taxon-constraints/evolutionary", "datamodels/taxon-constraints/id", "datamodels/taxon-constraints/index", "datamodels/taxon-constraints/label", "datamodels/taxon-constraints/never_in", "datamodels/taxon-constraints/only_in", "datamodels/taxon-constraints/predicate", "datamodels/taxon-constraints/predicates", "datamodels/taxon-constraints/present_in", "datamodels/taxon-constraints/present_in_ancestor_of", "datamodels/taxon-constraints/redundant", "datamodels/taxon-constraints/redundant_with", "datamodels/taxon-constraints/redundant_with_only_in", "datamodels/taxon-constraints/sources", "datamodels/taxon-constraints/subject", "datamodels/taxon-constraints/taxon", "datamodels/taxon-constraints/taxon-constraints", "datamodels/taxon-constraints/unsatisfiable", "datamodels/taxon-constraints/via_terms", "datamodels/text-annotator/Boolean", "datamodels/text-annotator/Curie", "datamodels/text-annotator/Date", "datamodels/text-annotator/DateOrDatetime", "datamodels/text-annotator/Datetime", "datamodels/text-annotator/Decimal", "datamodels/text-annotator/Double", "datamodels/text-annotator/Float", "datamodels/text-annotator/HasSpan", "datamodels/text-annotator/Integer", "datamodels/text-annotator/Jsonpath", "datamodels/text-annotator/Jsonpointer", "datamodels/text-annotator/Ncname", "datamodels/text-annotator/Nodeidentifier", "datamodels/text-annotator/Objectidentifier", "datamodels/text-annotator/Position", "datamodels/text-annotator/Sparqlpath", "datamodels/text-annotator/String", "datamodels/text-annotator/TextAnnotation", "datamodels/text-annotator/TextAnnotationConfiguration", "datamodels/text-annotator/TextAnnotationResultSet", "datamodels/text-annotator/TextualElement", "datamodels/text-annotator/Time", "datamodels/text-annotator/TransformationType", "datamodels/text-annotator/Uri", "datamodels/text-annotator/Uriorcurie", "datamodels/text-annotator/annotations", "datamodels/text-annotator/categories", "datamodels/text-annotator/confidence", "datamodels/text-annotator/id", "datamodels/text-annotator/include_aliases", "datamodels/text-annotator/index", "datamodels/text-annotator/info", "datamodels/text-annotator/is_longest_match", "datamodels/text-annotator/limit", "datamodels/text-annotator/match_string", "datamodels/text-annotator/match_type", "datamodels/text-annotator/matches_whole_text", "datamodels/text-annotator/model", "datamodels/text-annotator/object_aliases", "datamodels/text-annotator/object_categories", "datamodels/text-annotator/object_id", "datamodels/text-annotator/object_label", "datamodels/text-annotator/object_source", "datamodels/text-annotator/parent_document", "datamodels/text-annotator/predicate_id", "datamodels/text-annotator/source_text", "datamodels/text-annotator/sources", "datamodels/text-annotator/subject_end", "datamodels/text-annotator/subject_label", "datamodels/text-annotator/subject_source", "datamodels/text-annotator/subject_start", "datamodels/text-annotator/subject_text_id", "datamodels/text-annotator/text", "datamodels/text-annotator/text-annotator", "datamodels/text-annotator/token_exclusion_list", "datamodels/text-annotator/types", "datamodels/validation/Boolean", "datamodels/validation/ConstraintComponent", "datamodels/validation/Curie", "datamodels/validation/Date", "datamodels/validation/DateOrDatetime", "datamodels/validation/Datetime", "datamodels/validation/Decimal", "datamodels/validation/Double", "datamodels/validation/ExternalReferenceValidationResult", "datamodels/validation/Float", "datamodels/validation/Integer", "datamodels/validation/Jsonpath", "datamodels/validation/Jsonpointer", "datamodels/validation/MappingValidationResult", "datamodels/validation/NamedResource", "datamodels/validation/Ncname", "datamodels/validation/Node", "datamodels/validation/Nodeidentifier", "datamodels/validation/Objectidentifier", "datamodels/validation/RepairConfiguration", "datamodels/validation/RepairOperation", "datamodels/validation/RepairReport", "datamodels/validation/Report", "datamodels/validation/Result", "datamodels/validation/SeverityOptions", "datamodels/validation/Sparqlpath", "datamodels/validation/String", "datamodels/validation/Time", "datamodels/validation/TypeSeverityKeyValue", "datamodels/validation/Uri", "datamodels/validation/Uriorcurie", "datamodels/validation/ValidationConfiguration", "datamodels/validation/ValidationReport", "datamodels/validation/ValidationResult", "datamodels/validation/ValidationResultType", "datamodels/validation/category", "datamodels/validation/confidence", "datamodels/validation/dry_run", "datamodels/validation/http_response_code", "datamodels/validation/id", "datamodels/validation/index", "datamodels/validation/info", "datamodels/validation/instantiates", "datamodels/validation/max_number_results_per_type", "datamodels/validation/modified", "datamodels/validation/number_of_attempts", "datamodels/validation/object", "datamodels/validation/object_id", "datamodels/validation/object_info", "datamodels/validation/object_str", "datamodels/validation/predicate", "datamodels/validation/predicate_id", "datamodels/validation/problem", "datamodels/validation/prompt_info", "datamodels/validation/repairs", "datamodels/validation/results", "datamodels/validation/schema_path", "datamodels/validation/severity", "datamodels/validation/source", "datamodels/validation/subject", "datamodels/validation/subject_id", "datamodels/validation/subject_info", "datamodels/validation/successful", "datamodels/validation/suggested_modifications", "datamodels/validation/suggested_predicate", "datamodels/validation/time_checked", "datamodels/validation/type", "datamodels/validation/type_severity_map", "datamodels/validation/types", "datamodels/validation/url", "datamodels/validation/validation_configuration", "datamodels/validation/validaton-results", "faq/architecture", "faq/commandline", "faq/contributing", "faq/general", "faq/index", "faq/ontologies", "faq/troubleshooting", "glossary", "guide/aliases", "guide/associations", "guide/basics", "guide/curies-and-uris", "guide/index", "guide/learning-more", "guide/logical-definitions", "guide/mappings", "guide/obsoletion", "guide/primary-labels", "guide/relationships-and-graphs", 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1177, 1178, 1179, 1180, 1181, 1183], "incatool": [0, 495, 1100, 1106, 1124, 1163, 1192], "github": [0, 2, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 470, 471, 472, 473, 474, 475, 476, 480, 488, 495, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 1100, 1102, 1106, 1109, 1124, 1134, 1138, 1139, 1150, 1157, 1163, 1183, 1192], "io": [0, 388, 396, 400, 410, 412, 413, 418, 436, 1106, 1109, 1123, 1192], "access": [0, 1, 495, 1099, 1100, 1103, 1106, 1108, 1110, 1111, 1114, 1123, 1126, 1129, 1131, 1132, 1135, 1137, 1155, 1156, 1158, 1159, 1162, 1182, 1183, 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1178, 1180, 1181, 1182, 1192], "graph_traversal_method": 0, "whether": [0, 1106, 1107, 1115, 1116, 1119, 1137, 1141, 1145, 1161, 1166, 1167, 1168, 1169, 1170, 1171, 1175, 1176, 1178, 1181], "formal": [0, 1, 381, 437, 939, 955, 956, 1100, 1106, 1108, 1109, 1110, 1117, 1123, 1166, 1178], "entail": [0, 140, 153, 163, 842, 876, 882, 1100, 1106, 1111, 1113, 1131, 1166, 1173, 1178, 1179], "walk": [0, 1106, 1117, 1130, 1133, 1172], "hop": [0, 1106, 1117], "each": [0, 1, 140, 153, 161, 163, 202, 273, 321, 324, 331, 365, 437, 448, 827, 993, 1100, 1102, 1106, 1107, 1109, 1117, 1118, 1119, 1123, 1126, 1129, 1132, 1140, 1141, 1145, 1163, 1166, 1168, 1169, 1171, 1175, 1176, 1178, 1180, 1181, 1192], "piec": [0, 1, 1106, 1108, 1109, 1180], "text": [0, 109, 140, 148, 202, 214, 273, 324, 380, 397, 404, 406, 411, 476, 480, 488, 495, 505, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 575, 583, 667, 676, 685, 694, 698, 842, 860, 861, 882, 922, 978, 988, 989, 991, 993, 998, 1002, 1003, 1005, 1006, 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1167], "return": [0, 693, 717, 722, 989, 1001, 1004, 1107, 1110, 1113, 1114, 1115, 1116, 1117, 1129, 1132, 1140, 1141, 1142, 1144, 1145, 1146, 1149, 1162, 1165, 1166, 1167, 1168, 1169, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 1180, 1181, 1182, 1193], "repres": [0, 1, 18, 19, 27, 31, 46, 106, 107, 112, 118, 125, 142, 150, 151, 158, 162, 163, 202, 212, 217, 219, 220, 224, 234, 235, 236, 237, 239, 248, 267, 268, 272, 279, 280, 281, 314, 315, 323, 331, 333, 334, 373, 380, 382, 384, 385, 388, 389, 394, 398, 399, 400, 403, 405, 406, 411, 413, 414, 417, 418, 419, 421, 430, 431, 432, 436, 437, 438, 440, 441, 442, 443, 446, 448, 450, 451, 453, 454, 458, 463, 465, 466, 472, 473, 475, 525, 531, 544, 613, 690, 691, 701, 717, 735, 742, 758, 760, 761, 767, 780, 812, 833, 834, 841, 882, 934, 935, 936, 940, 943, 952, 953, 954, 967, 983, 984, 992, 1001, 1024, 1044, 1045, 1054, 1067, 1106, 1108, 1109, 1111, 1113, 1114, 1133, 1143, 1162, 1165, 1166, 1192], "gene2anat": 0, "g2t": 0, "u": [0, 1106, 1117, 1158], "recommend": [0, 212, 393, 402, 434, 452, 460, 480, 488, 530, 535, 540, 545, 695, 726, 1035, 1060, 1093, 1102, 1105, 1113, 1123, 1124, 1126, 1129, 1165, 1167, 1174, 1181, 1192], "alwai": [0, 1, 393, 460, 1105, 1106, 1126, 1129, 1165], "background": [0, 93, 116, 117, 125, 1111, 1117, 1167], "consid": [0, 2, 388, 396, 410, 412, 441, 476, 480, 484, 488, 499, 503, 509, 512, 521, 530, 532, 535, 540, 541, 545, 613, 641, 1113, 1115, 1141, 1159, 1165, 1166, 1177, 1178, 1179, 1192], "experi": [0, 1109], "subsum": [0, 941, 953, 963, 1175], "lower": [0, 1117], "alreadi": [0, 1118, 1129, 1149], "pseudo": 0, "fake": 0, "simpli": [0, 1109, 1116, 1136, 1171], "reflex": [0, 153, 163, 1106, 1117, 1118, 1172], "itself": [0, 1, 405, 1106, 1109, 1117], "summar": [0, 1113, 1123], "meaning": [0, 1117, 1129], "treat": [0, 28, 113, 159, 225, 274, 325, 415, 547, 693, 702, 737, 768, 843, 944, 994, 1056, 1100, 1106, 1107, 1108, 1115, 1118, 1131, 1135, 1145, 1165, 1179, 1192], "cutoff": [0, 92, 125, 128, 1167], "greater": [0, 1061, 1167], "05": [0, 1165, 1167], "sample_fil": 0, "b": [0, 384, 386, 388, 431, 437, 717, 735, 1117, 1118, 1124, 1129, 1162], "background_fil": 0, "allow": [0, 1, 411, 437, 465, 693, 717, 720, 1058, 1061, 1067, 1080, 1083, 1094, 1100, 1106, 1107, 1114, 1116, 1123, 1126, 1129, 1132, 1133, 1136, 1148, 1156, 1176, 1182], "well": [0, 1, 2, 31, 46, 388, 405, 437, 446, 1100, 1106, 1108, 1109, 1110, 1129, 1132, 1140, 1166, 1173, 1176], "attribute_slim": 0, "value_slim": 0, "sub": [0, 24, 44, 384, 437, 827, 842, 882, 1117, 1149, 1151, 1162], "singl": [0, 1, 93, 115, 116, 117, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 130, 132, 133, 388, 389, 393, 394, 424, 434, 437, 495, 1108, 1116, 1136, 1162, 1166, 1171, 1179, 1181, 1192], "node": [0, 18, 28, 46, 106, 113, 125, 140, 150, 159, 163, 179, 197, 219, 225, 234, 267, 274, 279, 314, 321, 325, 331, 372, 373, 380, 381, 382, 384, 385, 388, 389, 393, 394, 397, 398, 403, 404, 405, 406, 410, 411, 412, 415, 417, 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"wish": [0, 212, 213, 228, 1113, 1115, 1123, 1135, 1181], "fulli": [0, 1102, 1106, 1115, 1129, 1192, 1193], "anc": [0, 1100, 1117], "split": 0, "seed": [0, 1172, 1178], "Then": [0, 1117, 1123, 1126, 1129, 1130, 1133, 1135, 1159, 1178], "idfil": [0, 1118], "miss": [0, 140, 153, 163, 1113, 1117, 1124, 1149, 1166, 1181], "util": [0, 1106, 1127, 1141, 1143, 1148, 1150, 1151, 1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1165, 1166, 1167, 1168, 1169, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 1180, 1181], "table_fil": [0, 1164], "popul": [0, 1, 1113, 1119, 1145, 1166, 1171], "unpopul": 0, "row": [0, 1113], "revers": 0, "blank": [0, 1106, 1166], "scenario": [0, 1, 1166], "convent": [0, 3, 4, 17, 22, 23, 60, 84, 495, 1102, 1109, 1111, 1116, 1119, 1192], "header": 0, "later": [0, 2, 1117, 1118, 1129, 1165], "don": [0, 1, 2, 202, 1100, 1103, 1108, 1117, 1119, 1126, 1129, 1135, 1140, 1149, 1162, 1192], "By": [0, 1105, 1113, 1116, 1166, 1167], "throw": [0, 1172], "success": [0, 1047, 1067, 1129, 1174], "relax": [0, 418, 1166], "cannot": [0, 153, 163, 476, 480, 485, 488, 508, 509, 512, 521, 530, 533, 535, 540, 541, 545, 560, 1132, 1166], "remain": 0, "no_data": 0, "recogn": [0, 1107, 1126, 1180], "uniqu": [0, 1, 2, 153, 163, 164, 167, 173, 176, 217, 223, 230, 388, 396, 410, 412, 436, 437, 476, 485, 505, 509, 512, 521, 541, 625, 813, 816, 828, 835, 840, 842, 882, 1106, 1109, 1110, 1126, 1129, 1166], "procedur": 0, "denorm": [0, 41, 46, 1108], "foo_id": 0, "foo_nam": 0, "implicit": [0, 1108, 1182, 1193], "wai": [0, 1, 1099, 1102, 1104, 1106, 1107, 1108, 1109, 1110, 1113, 1114, 1115, 1116, 1118, 1119, 1123, 1124, 1126, 1129, 1133, 1135, 1141, 1162, 1163, 1165, 1167, 1176, 1181, 1182, 1192], "linkml": [0, 2, 8, 97, 137, 152, 169, 172, 178, 187, 190, 195, 200, 206, 254, 281, 293, 299, 333, 334, 335, 370, 377, 469, 492, 669, 680, 712, 713, 714, 715, 721, 741, 747, 810, 820, 850, 851, 852, 853, 858, 859, 878, 914, 925, 973, 1026, 1027, 1029, 1030, 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1119, 1120, 1128, 1166, 1182], "world": [1, 1108, 1181], "intend": [1, 717, 735, 1102, 1104, 1106, 1107, 1108, 1113, 1116, 1140, 1160, 1166, 1167, 1192], "lingua": 1, "franca": 1, "veri": [1, 1100, 1102, 1104, 1107, 1109, 1114, 1116, 1123, 1129, 1140, 1155], "keep": [1, 2, 21, 46, 77], "rang": [1, 3, 4, 17, 20, 21, 22, 23, 24, 28, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 92, 93, 94, 113, 115, 116, 117, 119, 120, 121, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 153, 157, 159, 161, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 212, 213, 217, 223, 225, 227, 228, 229, 230, 231, 232, 233, 235, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 249, 250, 262, 263, 264, 265, 269, 274, 276, 277, 278, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 294, 295, 307, 308, 309, 310, 311, 312, 316, 317, 318, 321, 322, 325, 327, 328, 329, 330, 332, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 371, 372, 373, 380, 381, 382, 384, 385, 386, 388, 389, 393, 394, 396, 402, 403, 405, 410, 411, 412, 415, 417, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 470, 471, 472, 473, 474, 475, 476, 479, 480, 481, 482, 483, 484, 485, 488, 489, 497, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 518, 519, 520, 521, 522, 526, 527, 530, 532, 533, 535, 536, 537, 540, 541, 542, 545, 547, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615, 616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 643, 644, 645, 646, 647, 648, 649, 650, 651, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 670, 671, 672, 673, 674, 677, 692, 693, 695, 696, 702, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 736, 737, 738, 739, 740, 743, 761, 764, 765, 766, 768, 771, 772, 773, 774, 775, 776, 777, 778, 779, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 811, 813, 815, 816, 817, 824, 825, 827, 828, 835, 838, 839, 840, 842, 843, 845, 846, 847, 848, 849, 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 860, 861, 862, 863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 883, 884, 885, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 911, 912, 913, 915, 916, 917, 918, 919, 920, 936, 939, 940, 941, 942, 944, 946, 947, 948, 949, 950, 951, 952, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 965, 966, 968, 969, 978, 988, 989, 990, 991, 994, 996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020, 1021, 1022, 1023, 1025, 1028, 1035, 1040, 1041, 1043, 1046, 1047, 1048, 1049, 1050, 1055, 1056, 1058, 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1096, 1097, 1102, 1108, 1123, 1129, 1156, 1182], "address": [1, 1106], "user": [1, 394, 424, 693, 707, 709, 710, 716, 717, 718, 719, 720, 722, 731, 737, 739, 1102, 1107, 1109, 1113, 1117, 1118, 1129, 1132, 1141, 1162, 1178, 1180, 1182], "quit": [1, 1165], "straightforward": 1, "someth": [1, 212, 227, 406, 523, 613, 1104, 1106, 1107, 1108, 1123, 1126], "paper": 1, "2000": 1, "thousand": [1, 1141], "inter": [1, 1142], "term": [1, 4, 31, 46, 50, 55, 69, 70, 93, 115, 121, 125, 212, 228, 234, 262, 264, 269, 273, 276, 277, 279, 280, 283, 284, 286, 287, 288, 289, 292, 307, 309, 318, 324, 328, 329, 331, 333, 346, 347, 351, 356, 359, 362, 369, 388, 393, 406, 425, 434, 437, 442, 443, 448, 460, 476, 480, 484, 485, 488, 499, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 521, 522, 526, 527, 530, 532, 533, 535, 540, 542, 545, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 582, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 620, 623, 625, 635, 646, 647, 652, 655, 657, 658, 660, 664, 665, 666, 668, 693, 695, 698, 717, 720, 725, 726, 728, 729, 737, 739, 765, 766, 771, 772, 773, 774, 775, 776, 777, 778, 780, 783, 791, 792, 793, 794, 795, 796, 797, 799, 802, 803, 804, 805, 806, 807, 936, 939, 940, 941, 950, 952, 953, 954, 955, 956, 958, 959, 960, 965, 968, 969, 993, 1106, 1107, 1108, 1109, 1113, 1115, 1117, 1118, 1119, 1123, 1128, 1130, 1133, 1136, 1137, 1141, 1149, 1165, 1166, 1167, 1171, 1175, 1176, 1177, 1178, 1180, 1181, 1182, 1192, 1193], "howev": [1, 1102, 1104, 1106, 1107, 1108, 1110, 1113, 1117, 1118, 1119, 1123, 1129, 1131, 1141, 1162, 1192], "turn": [1, 1116, 1191], "flexibl": [1, 1106], "malleabl": 1, "prov": [1, 212, 247, 249, 294, 476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569, 813, 839, 845, 875, 907, 919, 1059], "logic": [1, 388, 394, 428, 437, 442, 480, 485, 495, 510, 511, 527, 530, 536, 550, 551, 552, 553, 554, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 573, 575, 576, 577, 578, 580, 582, 583, 584, 586, 587, 588, 589, 591, 592, 593, 594, 596, 597, 598, 599, 600, 601, 602, 603, 606, 607, 608, 609, 610, 612, 613, 616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 635, 637, 646, 647, 649, 652, 655, 657, 658, 660, 663, 664, 665, 666, 668, 671, 842, 872, 882, 1100, 1104, 1106, 1108, 1109, 1111, 1117, 1131, 1166, 1172, 1181, 1192], "artifact": 1, "countri": 1, "knowledg": [1, 3, 4, 17, 21, 22, 30, 46, 78, 1104, 1106, 1109, 1118, 1123, 1129, 1130, 1131, 1163, 1165], "entireti": 1, "wikidata": [1, 1055, 1131], "try": [1, 1105, 1129, 1130, 1135, 1136, 1182, 1192], "pluralist": [1, 1099, 1106, 1107, 1132, 1192], "appropri": [1, 1131, 1136], "abstract": [1, 22, 249, 294, 372, 405, 482, 535, 541, 542, 565, 590, 613, 614, 628, 629, 641, 650, 653, 656, 662, 674, 761, 780, 781, 800, 840, 846, 863, 881, 882, 897, 920, 942, 1049, 1050, 1067, 1106, 1116, 1129, 1132, 1135, 1140, 1143, 1161, 1170, 1175], "commun": [1, 1106, 1111, 1114, 1136], "serv": [1, 1106, 1109, 1137, 1140, 1163, 1166, 1171], "classic": [1, 1118], "those": [1, 212, 227, 394, 420, 437, 1106, 1108, 1114, 1166, 1172], "conceiv": [1, 1118, 1132, 1172], "loos": [1, 1106], "thought": [1, 1117, 1192], "persist": [1, 1106, 1136], "variou": [1, 1106, 1118, 1129, 1136, 1186], "metadata": [1, 4, 50, 202, 212, 227, 228, 229, 231, 234, 237, 239, 240, 241, 242, 247, 372, 373, 380, 381, 382, 384, 385, 388, 389, 393, 394, 396, 403, 405, 411, 417, 437, 443, 505, 575, 625, 642, 842, 847, 882, 1106, 1108, 1109, 1111, 1114, 1119, 1120, 1127, 1131, 1149, 1166, 1171, 1172, 1174, 1176, 1181], "associ": [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 202, 402, 405, 437, 440, 443, 444, 450, 472, 473, 475, 839, 882, 919, 1099, 1106, 1107, 1111, 1118, 1127, 1158, 1159, 1161, 1162, 1164, 1166, 1167, 1170, 1182], "predomin": 1, "purpos": [1, 202, 388, 396, 410, 412, 441, 510, 511, 527, 540, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 582, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 620, 623, 625, 635, 646, 647, 652, 655, 657, 658, 664, 665, 666, 668, 717, 735, 1106, 1107, 1108, 1110, 1113, 1117, 1123, 1135, 1140], "necessarili": [1, 1106, 1192], "disjoint": [1, 381, 422, 423, 428, 437, 471, 1106, 1166, 1172, 1173], "categori": [1, 140, 153, 163, 212, 234, 476, 480, 488, 502, 509, 512, 520, 521, 530, 535, 540, 541, 545, 613, 614, 693, 717, 827, 842, 850, 856, 882, 989, 1001, 1040, 1067, 1106, 1117, 1163, 1166], "ambigu": [1, 1106, 1108, 1166], "equat": [1, 381, 437, 470, 1106], "broadli": [1, 1106, 1118], "encompass": [1, 31, 46, 1106, 1166], "scotland": 1, "denot": [1, 1106, 1107, 1109], "strictli": [1, 1105], "three": [1, 1102, 1108], "datatypeproperti": [1, 404, 842, 868, 1106, 1166], "discrimin": 1, "confus": [1, 1103, 1106, 1117, 1182], "ask": [1, 1108, 1117, 1123, 1132, 1166], "think": [1, 1106, 1192], "would": [1, 217, 223, 232, 233, 1102, 1106, 1111, 1113, 1115, 1117, 1118, 1123, 1126, 1140, 1192], "accustom": 1, "stand": [1, 1102, 1109, 1117], "alon": 1, "monolith": 1, "make": [1, 827, 1099, 1101, 1105, 1106, 1107, 1108, 1116, 1117, 1118, 1119, 1123, 1124, 1126, 1129, 1130, 1135, 1136, 1141, 1192], "assumpt": [1, 153, 163, 1116, 1119], "fact": [1, 1109, 1113, 1117, 1129, 1140], "organ": [1, 827, 853, 1106, 1109, 1117, 1163, 1191], "modular": 1, "compon": [1, 495, 613, 1115, 1126, 1172, 1180], "much": [1, 1103, 1140, 1192], "softwar": [1, 1126, 1133], "evolv": 1, "program": [1, 1106, 1109, 1126, 1129, 1130], "incorpor": [1, 1117, 1129], "design": [1, 163, 173, 191, 202, 1103, 1106, 1117, 1123, 1127, 1140, 1145], "worri": [1, 1099, 1129, 1140, 1170], "everyth": [1, 437, 448, 1100, 1106, 1109, 1110, 1117], "were": [1, 1115, 1123, 1131, 1153, 1166], "actual": [1, 942, 953, 1099, 1106, 1117], "let": [1, 1117, 1130], "explor": [1, 1111, 1112, 1118, 1176], "composit": 1, "driven": [1, 1124], "infrastructur": 1, "web": [1, 1104, 1106, 1109, 1110, 1116, 1131, 1133, 1192], "stack": 1, "scienc": [1, 1106, 1129], "bioinformat": [1, 1106, 1117, 1132, 1151], "bridg": [1, 1131], "essenti": [1, 1117], "expand": [1, 6, 95, 135, 204, 252, 273, 297, 324, 375, 490, 678, 745, 818, 923, 971, 993, 1029, 1166, 1172, 1174], "contract": [1, 1166], "seem": [1, 1113, 1140], "surpris": [1, 1129], "construct": [1, 372, 437, 1102, 1106, 1109, 1117, 1119, 1145, 1166, 1192], "call": [1, 1103, 1106, 1108, 1118, 1129, 1136, 1140, 1148, 1166, 1191], "owlinterfac": [1, 202, 1128, 1150, 1170, 1173], "rdfinterfac": 1, "common": [1, 31, 46, 316, 371, 765, 771, 780, 1104, 1106, 1107, 1109, 1113, 1115, 1116, 1117, 1118, 1127, 1129, 1137, 1140, 1141, 1170, 1177], "opaqu": 1, "exactli": [1, 140, 153, 161, 163, 164, 1141], "human": [1, 31, 46, 147, 163, 165, 388, 394, 396, 410, 412, 437, 441, 509, 510, 511, 517, 523, 527, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 625, 635, 646, 647, 655, 658, 664, 665, 666, 668, 694, 936, 939, 940, 942, 953, 954, 1106, 1107, 1108, 1109, 1110, 1111, 1117, 1118, 1192], "represent": [1, 6, 95, 135, 204, 252, 297, 375, 417, 437, 448, 487, 490, 546, 613, 678, 745, 818, 923, 971, 1029, 1106, 1109, 1111, 1115, 1117, 1118, 1159, 1167], "univers": [1, 382, 388, 419, 437, 1107, 1116], "preflabel": [1, 217, 232, 476, 485, 505, 509, 512, 521, 541, 625, 988, 1012, 1106, 1116, 1192], "share": [1, 200, 262, 279, 287, 290, 293, 307, 331, 356, 364, 370, 469, 669, 741, 810, 914, 1026, 1095, 1105, 1106, 1108, 1114, 1118, 1166], "multipl": [1, 212, 213, 227, 382, 389, 394, 419, 424, 429, 437, 443, 448, 451, 457, 693, 737, 765, 771, 1049, 1067, 1082, 1106, 1107, 1108, 1116, 1118, 1120, 1129, 1148, 1162, 1163, 1166, 1176, 1179, 1182, 1192, 1193], "intent": [1, 1166, 1192], "languag": [1, 373, 380, 405, 411, 417, 437, 440, 613, 614, 1104, 1106, 1111, 1116, 1120, 1127, 1136, 1166, 1170, 1182, 1192], "unintent": 1, "version": [1, 2, 153, 163, 394, 437, 673, 695, 717, 729, 835, 842, 854, 882, 918, 1107, 1110, 1117, 1120, 1129, 1166, 1171, 1182], "freedom": 1, "littl": [1, 1129, 1140], "disallow": 1, "suit": [1, 1106, 1119], "qc": [1, 1132, 1181], "dashboard": 1, "aim": [1, 1100, 1107, 1192], "conveni": [1, 1102, 1106, 1108, 1166], "certain": [1, 1102, 1110, 1166], "ol": [1, 1102, 1106, 1113, 1128, 1136, 1137, 1152, 1164, 1166], "roughli": [1, 1117], "adher": [1, 1106, 1132], "welcom": [2, 1100, 1101, 1103, 1128], "tracker": [2, 1100, 1120], "bug": [2, 1101, 1119, 1145], "enhanc": [2, 1123], "tutori": [2, 1103, 1111, 1117, 1125, 1127, 1129, 1130, 1133, 1135, 1162, 1193], "resid": 2, "folder": [2, 1100, 1102, 1124, 1129, 1135, 1149], "build": [2, 263, 279, 285, 308, 331, 348, 1106, 1118, 1126, 1128, 1162, 1180], "live": [2, 476, 480, 488, 499, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 613, 1124], "diataxi": 2, "rst": 2, "md": [2, 1102], "docstr": [2, 1102], "read": [2, 1104, 1109, 1111, 1136], "architectur": [2, 1103, 1127, 1129, 1164], "best": [2, 1105, 1118, 1123, 1165, 1182], "practic": [2, 1105, 1107, 1113, 1115, 1116, 1118, 1166, 1192], "sooner": 2, "mark": [2, 1115, 1117], "draft": 2, "readi": [2, 1124, 1128], "review": [2, 1113, 1123], "sure": [2, 1126, 1129], "unit": [2, 263, 278, 279, 285, 308, 321, 330, 331, 348, 365, 1102], "print": [2, 1099, 1107, 1110, 1114, 1115, 1116, 1117, 1126, 1130, 1131, 1137, 1140, 1141, 1145, 1148, 1154, 1156, 1158, 1159, 1165, 1166, 1167, 1170, 1171, 1172, 1176, 1180, 1192], "ing": 2, "log": [2, 780, 781, 1118], "diagnost": [2, 1118], "captur": [2, 372, 437, 443, 1108, 1166], "exemplar": 2, "regist": [2, 418], "scheme": [2, 1126, 1154, 1160, 1162, 1164], "__init__": [2, 1156, 1157, 1161, 1163], "py": [2, 812, 1130, 1150, 1156, 1157, 1159, 1160, 1161, 1162, 1163, 1173], "__post_init__": [2, 1126], "cli": [2, 1102, 1120, 1123, 1129, 1141, 1182, 1192], "refactor": 2, "substanti": 2, "ad": [2, 212, 227, 234, 1107, 1112, 1113, 1117, 1123, 1126, 1136, 1137, 1138], "diff": [2, 4, 42, 46, 56, 71, 89, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 158, 159, 160, 161, 164, 165, 166, 167, 168, 170, 171, 173, 174, 175, 176, 177, 179, 180, 181, 182, 183, 184, 185, 186, 188, 189, 191, 192, 193, 194, 196, 197, 198, 199, 202, 815, 828, 840, 842, 863, 879, 880, 882, 1106, 1127, 1168, 1170, 1174], "coordin": 2, "advanc": [2, 1102, 1106, 1107, 1112, 1117, 1128, 1135, 1151, 1166, 1180], "dev": [2, 1135], "environ": [2, 1109, 1123, 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"predef": [394, 437], "insubset": [394, 464, 476, 480, 488, 502, 509, 512, 521, 530, 535, 540, 541, 545, 612], "versioninfo": [394, 474, 533, 613, 674, 835, 918], "histor": [394, 424, 1107, 1108, 1109, 1114], "carri": [394, 424], "awar": [394, 424], "0000115": [394, 426, 476, 480, 488, 505, 509, 512, 521, 530, 535, 540, 541, 545, 575, 1115], "predefin": [394, 420], "propertytyp": [396, 404, 437], "propertytypeenum": [396, 437, 456], "namedindividu": [397, 476, 480, 484, 488, 506, 509, 510, 511, 512, 526, 527, 530, 532, 533, 535, 540, 541, 542, 545, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 625, 635, 646, 647, 655, 658, 663, 664, 665, 666, 668, 824, 827, 838, 842, 892, 1166], "prefixedid": 400, "unprefixedid": 400, "info": [401, 407, 824, 827, 835, 838, 882, 918, 988, 1001, 1035, 1040, 1047, 1051, 1058, 1060, 1067, 1080, 1100, 1107, 1110, 1124, 1129, 1135, 1137], "hasexactsynonym": [401, 406, 476, 480, 485, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 600, 1104, 1107, 1115], "hasnarrowsynonym": [401, 406, 476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 601, 1107], "hasbroadsynonym": [401, 406, 476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 598, 1107], "hasrelatedsynonym": [401, 406, 476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 606, 1104, 1107], "go_": [402, 437, 1166], "strongli": [402, 452], "r1": [403, 437], "rn": [403, 437], "chainpredicateid": [403, 437], "claus": [403, 421, 437], "prope": [403, 437], "broader": [406, 1106, 1129], "bu": 406, "subsetproperti": [410, 1166], "synonymtyp": [411, 412, 437, 438, 1107], "synonymtypeidentifierstr": [411, 437, 465], "isexact": [411, 437], "scopeenum": [411, 437], "commonli": [413, 1106, 1192], "plain": [413, 698, 1107], "pmid": [417, 1108, 1129], "12345": 417, "registri": [418, 1182], "bioregistri": 418, "usag": [419, 429, 437, 443, 451, 457, 1106, 1107, 1109, 1118, 1128, 1129, 1164, 1174], "propert": [419, 429, 443, 451, 457], "principl": [437, 448, 1035, 1060, 1093, 1117], "attach": [437, 448, 694, 1166, 1174], "metedata": [437, 448], "Not": [437, 448, 1117, 1140, 1157], "obographs_datamodel": 437, "expr": 437, "nodetypeenum": 437, "objec": [440, 443, 450, 472, 473, 475], "benchmark": 449, "scopesenum": 461, "namedobject": [476, 480, 485, 488, 509, 512, 521, 530, 533, 535, 540, 541, 542, 545, 552, 608, 613, 668], "hassynonym": [476, 480, 481, 485, 488, 509, 510, 511, 512, 521, 522, 527, 530, 535, 540, 541, 545, 550, 584, 598, 600, 601, 606, 613, 662], "haslifecycl": [476, 480, 481, 484, 488, 509, 512, 521, 522, 526, 530, 532, 535, 540, 541, 542, 545, 563, 578, 591, 592, 593, 596, 603, 613, 658, 665], "hasproven": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 533, 535, 540, 541, 545, 564, 566, 567, 568, 569, 572, 576, 583, 610, 613, 617, 646, 664, 666], "hasmap": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 535, 540, 541, 542, 545, 555, 559, 571, 588, 613, 635], "hascategori": [476, 480, 481, 488, 509, 512, 521, 522, 530, 535, 540, 541, 542, 545, 557, 562, 602, 612, 613], "hasuserinform": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 533, 535, 540, 541, 542, 545, 560, 570, 577, 589, 599, 609, 613, 647, 655], "hasminimalmetadata": [476, 480, 481, 485, 488, 509, 512, 521, 522, 530, 535, 540, 541, 545, 575, 613, 625], "has_exact_synonym": [476, 480, 485, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613, 662], "labeltyp": [476, 480, 485, 488, 505, 507, 509, 512, 521, 530, 535, 540, 541, 545, 598, 600, 601, 606, 613, 625, 662], "has_narrow_synonym": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613, 662], "has_broad_synonym": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613, 662], "has_related_synonym": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 613], "alternative_term": [476, 477, 480, 488, 507, 509, 510, 511, 512, 521, 527, 530, 535, 540, 541, 545, 584, 598, 600, 601, 613, 662], "isa_alternative_term": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 550, 613], "iedb_alternative_term": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 550, 613], "editor_preferred_term": [476, 480, 488, 507, 509, 512, 521, 528, 530, 535, 540, 541, 545, 550, 613], "obo_foundry_unique_label": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 550, 613], "has_obsolescence_reason": [476, 480, 488, 503, 509, 512, 521, 530, 532, 535, 540, 541, 545, 613, 641], "term_replaced_bi": [476, 477, 480, 484, 488, 499, 503, 509, 512, 521, 528, 530, 532, 535, 540, 541, 545, 613, 641], "has_alternative_id": [476, 480, 488, 499, 503, 509, 512, 521, 526, 530, 535, 540, 541, 545, 613, 641], "excluded_from_qc_check": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 542, 545, 590, 613], "excluded_subclassof": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 590, 613], 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521, 530, 535, 540, 541, 545, 613, 650], "term_tracker_item": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "broadmatch": [476, 480, 488, 504, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 629], "closematch": [476, 480, 488, 504, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 629, 694, 1129], "narrowmatch": [476, 480, 488, 504, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 629], "database_cross_refer": [476, 480, 485, 488, 504, 509, 512, 521, 530, 535, 540, 541, 545, 613, 629], "curieliter": [476, 480, 485, 488, 504, 509, 512, 521, 530, 535, 540, 541, 545, 571, 613], "has_obo_namespac": [476, 480, 488, 502, 509, 512, 521, 530, 535, 540, 541, 545, 613], "in_subset": [476, 480, 485, 488, 502, 503, 505, 506, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 563, 575, 576, 578, 584, 589, 596, 613, 625, 665], "conformsto": [476, 480, 488, 502, 509, 512, 521, 530, 535, 540, 541, 542, 545, 613, 614], "example_of_usag": [476, 477, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614], "curator_not": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 650], "has_curation_statu": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614], "depicted_bi": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614], "page": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 613, 614, 1106, 1109], "transitiveproperti": [476, 484, 488, 510, 511, 512, 521, 526, 527, 530, 532, 533, 535, 540, 542, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 580, 582, 583, 584, 586, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 616, 617, 620, 621, 623, 624, 625, 635, 646, 647, 649, 652, 655, 657, 658, 663, 664, 665, 666, 668, 1166], "homosapien": [476, 484, 488, 510, 511, 512, 521, 526, 527, 532, 533, 540, 542, 550, 555, 557, 559, 560, 562, 563, 564, 566, 567, 568, 569, 570, 571, 572, 575, 576, 577, 578, 583, 584, 588, 589, 591, 592, 593, 596, 598, 599, 600, 601, 602, 603, 606, 608, 609, 610, 612, 613, 617, 625, 635, 646, 647, 655, 658, 664, 665, 666, 668], "orcid": [476, 509, 1107], "omoschema": [476, 479, 480, 481, 482, 483, 484, 485, 488, 489, 495, 497, 502, 503, 504, 505, 506, 507, 508, 509, 512, 521, 522, 526, 530, 532, 533, 535, 536, 537, 540, 541, 542, 545, 554, 565, 579, 590, 591, 592, 593, 605, 608, 614, 628, 629, 630, 638, 641, 648, 650, 653, 656, 658, 674], "id_prefix": [476, 509, 936, 940, 1166], "disjoint_with": [476, 480, 485, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 600], "allotrop": [476, 477, 478, 480, 485, 488, 503, 505, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 575, 578, 589, 625, 665], "permit": [476, 480, 485, 488, 503, 506, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 563, 576, 578, 584, 589, 596, 665], "profil": [476, 480, 485, 488, 503, 505, 506, 507, 508, 509, 512, 521, 530, 535, 540, 541, 545, 550, 558, 563, 575, 576, 578, 584, 589, 596, 625, 665, 842, 872, 882, 1110, 1116, 1118, 1178], "0001847": [476, 480, 488, 507, 509, 511, 512, 521, 530, 535, 540, 541, 545], "9991118": [476, 480, 488, 507, 509, 510, 512, 521, 530, 535, 540, 541, 545], "0000111": [476, 480, 488, 507, 509, 512, 521, 530, 535, 540, 541, 545, 584], "uniquekei": [476, 480, 488, 507, 509, 512, 521, 527, 530, 535, 540, 541, 545], "0000589": [476, 480, 488, 507, 509, 512, 521, 527, 530, 535, 540, 541, 545], "obsoletion_related_properti": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 563, 578, 596, 603, 613, 665], "obsoleteaspect": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 563, 578, 603, 613, 665], "0000231": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 603, 1115], "isreplacedbi": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 665], "0100001": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 665, 1115, 1166], "owlc": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596], "owlapi": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 1173], "317": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596], "notobsoleteaspect": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 613], "hasalternativeid": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 596, 1115], "excluded_axiom": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 591, 592, 593, 613, 658], "hiddensynonym": [476, 480, 488, 503, 509, 512, 521, 530, 535, 540, 541, 545, 593], "2022": [476, 480, 485, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 567, 568, 1151], "04": [476, 480, 485, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 567, 568], "12": [476, 480, 485, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 567, 568], "deprecated_element_has_exact_replac": [476, 480, 485, 488, 506, 509, 512, 518, 519, 520, 521, 530, 535, 540, 541, 545, 567, 568, 624, 640], "provenance_properti": [476, 480, 485, 488, 506, 508, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 566, 567, 568, 569, 570, 572, 573, 576, 583, 597, 610, 613, 646, 660, 664, 666], "wasattributedto": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "structured_pattern": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "orcid_regex": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "interpol": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "partial_match": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 564, 569], "pav": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 566, 572, 617, 673], "createdon": [476, 480, 488, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 566], "authoredon": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 572], "importedfrom": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 617], "0000116": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 583], "narr": [476, 480, 488, 505, 506, 509, 512, 521, 530, 533, 535, 540, 541, 545, 575, 583, 667], "0000117": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 664], "0000119": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 576], "0000234": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 646], "0000412": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 610], "0000233": [476, 480, 488, 506, 509, 512, 521, 530, 535, 540, 541, 545, 666], "informative_properti": [476, 480, 485, 488, 502, 508, 509, 512, 521, 530, 533, 535, 540, 541, 545, 557, 558, 560, 562, 574, 577, 589, 599, 604, 609, 613, 626, 627, 647], "sdo": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 609], "0000112": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 589], "0000232": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 570], "0000114": [476, 480, 488, 508, 509, 512, 521, 530, 535, 540, 541, 545, 599], "foaf": 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"is_metadata_tag": [480, 530, 535, 540, 545, 613], "annotatedproperti": [480, 485, 613, 653], "has_synonym_typ": [480, 485, 613], "root": [482, 613, 1106, 1129, 1166, 1170, 1172, 1179], "anonymousclassexpress": [482, 537, 613], "anonym": [483, 537, 613, 842, 848, 849, 882, 883, 1113, 1166], "annotatedtarget": [484, 485, 613, 653], "annotatedsourc": [485, 522, 613, 653], "is_inf": [485, 613], "has_axiom_label": [485, 542, 613, 650], "is_a_defining_property_chain_axiom": [485, 613], "is_a_defining_property_chain_axiom_where_second_argument_is_reflex": [485, 613], "date_retriev": [485, 613, 650], "external_ontologi": [485, 613], "reification_pred": [485, 551, 552, 553, 613], "dc": [485, 533, 660], "0010000": [485, 597], "0002581": [485, 618], "0002582": [485, 619], "hassynonymtyp": [485, 607], "never_in_taxon": [488, 613], "disconnected_from": [488, 613, 656], "has_rank": [488, 542, 613], "disjointwith": [488, 489, 530, 536, 537, 545, 613, 628], "intersectionof": [488, 489, 537, 613, 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has_narrow_synonym": [[601, "slot-has-narrow-synonym"]], "Slot: has_obo_namespace": [[602, "slot-has-obo-namespace"]], "Slot: has_obsolescence_reason": [[603, "slot-has-obsolescence-reason"]], "Slot: has_ontology_root_term": [[604, "slot-has-ontology-root-term"]], "Slot: has_rank": [[605, "slot-has-rank"]], "Slot: has_related_synonym": [[606, "slot-has-related-synonym"]], "Slot: has_synonym_type": [[607, "slot-has-synonym-type"]], "Slot: image": [[609, "slot-image"]], "Slot: imported_from": [[610, "slot-imported-from"]], "Slot: imports": [[611, "slot-imports"]], "Slot: in_subset": [[612, "slot-in-subset"]], "Ontology Metadata Ontology Schema": [[613, "ontology-metadata-ontology-schema"]], "Slot: informative_property": [[614, "slot-informative-property"]], "Slot: intersectionOf": [[615, "slot-intersectionof"]], "Slot: inverseOf": [[616, "slot-inverseof"]], "Slot: isDefinedBy": [[617, "slot-isdefinedby"]], "Slot: is_a_defining_property_chain_axiom": [[618, 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[[636, "slot-never-in-taxon"]], "Slot: notes": [[637, "slot-notes"]], "Slot: oboInOwl_id": [[639, "slot-oboinowl-id"]], "Slot: oboInOwl_ontology": [[640, "slot-oboinowl-ontology"]], "Slot: obsoletion_related_property": [[641, "slot-obsoletion-related-property"]], "omo-schema": [[642, "omo-schema"]], "Slot: onClass": [[643, "slot-onclass"]], "Slot: onProperty": [[644, "slot-onproperty"]], "Slot: oneOf": [[645, "slot-oneof"]], "Slot: ontology_term_requester": [[646, "slot-ontology-term-requester"]], "Slot: page": [[647, "slot-page"]], "Slot: propertyChainAxiom": [[649, "slot-propertychainaxiom"]], "Slot: provenance_property": [[650, "slot-provenance-property"]], "Slot: qualifiedCardinality": [[651, "slot-qualifiedcardinality"]], "Slot: range": [[652, "slot-range"]], "Slot: reification_predicate": [[653, "slot-reification-predicate"]], "Slot: sameAs": [[654, "slot-sameas"]], "Slot: seeAlso": [[655, "slot-seealso"]], "Slot: shortcut_annotation_property": [[656, "slot-shortcut-annotation-property"]], "Slot: shorthand": [[657, "slot-shorthand"]], "Slot: should_conform_to": [[658, "slot-should-conform-to"]], "Slot: someValuesFrom": [[659, "slot-somevaluesfrom"]], "Slot: subClassOf": [[661, "slot-subclassof"]], "Slot: synonym": [[662, "slot-synonym"]], "Slot: temporal_interpretation": [[663, "slot-temporal-interpretation"]], "Slot: term_editor": [[664, "slot-term-editor"]], "Slot: term_replaced_by": [[665, "slot-term-replaced-by"]], "Slot: term_tracker_item": [[666, "slot-term-tracker-item"]], "Slot: title": [[667, "slot-title"], [913, "slot-title"]], "Slot: unionOf": [[670, "slot-unionof"]], "Slot: versionIRI": [[672, "slot-versioniri"]], "Slot: versionInfo": [[673, "slot-versioninfo"]], "Slot: version_property": [[674, "slot-version-property"]], "Enum: BooleanOperator": [[676, "enum-booleanoperator"]], "Class: ComplexQuery": [[677, "class-complexquery"]], "Enum: GraphFunction": [[685, "enum-graphfunction"]], "Class: PathExpression": [[692, 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include_obsoletes_in_results": [[716, "slot-include-obsoletes-in-results"]], "search datamodel": [[717, "search-datamodel"]], "Slot: is_complete": [[718, "slot-is-complete"]], "Slot: is_fuzzy": [[719, "slot-is-fuzzy"]], "Slot: is_partial": [[720, "slot-is-partial"]], "Slot: is_regular_expression": [[721, "slot-is-regular-expression"]], "Slot: limit": [[722, "slot-limit"], [1004, "slot-limit"]], "Slot: matches_full_search_term": [[723, "slot-matches-full-search-term"]], "Slot: none_of": [[724, "slot-none-of"]], "Slot: object_id": [[725, "slot-object-id"], [793, "slot-object-id"], [1011, "slot-object-id"], [1074, "slot-object-id"]], "Slot: object_match_field": [[727, "slot-object-match-field"]], "Slot: object_source": [[728, "slot-object-source"], [796, "slot-object-source"], [1013, "slot-object-source"]], "Slot: object_source_version": [[729, "slot-object-source-version"]], "Slot: path_to": [[730, "slot-path-to"]], "Slot: properties": [[731, "slot-properties"]], "Slot: result_count": [[733, "slot-result-count"]], "search-datamodel": [[735, "search-datamodel"]], "Slot: search_term": [[736, "slot-search-term"]], "Slot: search_terms": [[737, "slot-search-terms"]], "Slot: snippet": [[738, "slot-snippet"]], "Slot: syntax": [[739, "slot-syntax"]], "Slot: traversal": [[740, "slot-traversal"]], "SemSQL": [[742, "semsql"]], "Class: BestMatch": [[743, "class-bestmatch"]], "Type: ItemCount": [[753, "type-itemcount"]], "Type: NegativeLogValue": [[757, "type-negativelogvalue"]], "Type: NonNegativeFloat": [[759, "type-nonnegativefloat"]], "Class: PairwiseSimilarity": [[761, "class-pairwisesimilarity"]], "Class: TermInfo": [[764, "class-terminfo"]], "Class: TermPairwiseSimilarity": [[765, "class-termpairwisesimilarity"]], "Class: TermSetPairwiseSimilarity": [[766, "class-termsetpairwisesimilarity"]], "Type: ZeroToOne": [[770, "type-zerotoone"]], "Slot: ancestor_id": [[771, "slot-ancestor-id"]], "Slot: ancestor_information_content": [[772, "slot-ancestor-information-content"]], "Slot: ancestor_label": [[773, "slot-ancestor-label"]], "Slot: ancestor_source": [[774, "slot-ancestor-source"]], "Slot: average_score": [[775, "slot-average-score"]], "Slot: best_score": [[776, "slot-best-score"]], "Slot: cosine_similarity": [[777, "slot-cosine-similarity"]], "Slot: dice_similarity": [[778, "slot-dice-similarity"]], "Semantic Similarity": [[780, "semantic-similarity"]], "Slot: information_content": [[781, "slot-information-content"]], "Slot: intersection_count": [[782, "slot-intersection-count"]], "Slot: jaccard_similarity": [[783, "slot-jaccard-similarity"]], "Slot: match_source": [[785, "slot-match-source"]], "Slot: match_source_label": [[786, "slot-match-source-label"]], "Slot: match_subsumer": [[787, "slot-match-subsumer"]], "Slot: match_subsumer_label": [[788, "slot-match-subsumer-label"]], "Slot: match_target": [[789, "slot-match-target"]], "Slot: match_target_label": [[790, "slot-match-target-label"]], "Slot: metric": [[791, "slot-metric"]], "Slot: object_best_matches": [[792, "slot-object-best-matches"]], "Slot: object_information_content": [[794, "slot-object-information-content"]], "Slot: object_termset": [[797, "slot-object-termset"]], "Slot: overlap_coefficient": [[798, "slot-overlap-coefficient"]], "Slot: phenodigm_score": [[799, "slot-phenodigm-score"]], "Slot: score": [[800, "slot-score"]], "Slot: similarity": [[801, "slot-similarity"]], "Slot: subject_best_matches": [[802, "slot-subject-best-matches"]], "Slot: subject_id": [[803, "slot-subject-id"], [1087, "slot-subject-id"]], "Slot: subject_information_content": [[804, "slot-subject-information-content"]], "Slot: subject_source": [[806, "slot-subject-source"], [1020, "slot-subject-source"]], "Slot: subject_termset": [[807, "slot-subject-termset"]], "Slot: subsumed_by_score": [[808, "slot-subsumed-by-score"]], "Slot: subsumes_score": [[809, "slot-subsumes-score"]], "Slot: union_count": [[811, "slot-union-count"]], "SSSOM": [[812, "sssom"], [1114, "sssom"]], "Class: ChangeTypeStatistic": [[815, "class-changetypestatistic"]], "Class: ContributorRole": [[816, "class-contributorrole"]], "Class: ContributorStatistics": [[817, "class-contributorstatistics"]], "Class: FacetStatistics": [[824, "class-facetstatistics"]], "LinkML Specification": [[824, "linkml-specification"], [827, "linkml-specification"], [838, "linkml-specification"]], "Class: FacetedCount": [[825, "class-facetedcount"]], "Class: GlobalStatistics": [[827, "class-globalstatistics"]], "Class: GroupedStatistics": [[828, "class-groupedstatistics"]], "Class: SummaryStatisticCollection": [[838, "class-summarystatisticcollection"]], "Class: SummaryStatisticsCalculationActivity": [[839, "class-summarystatisticscalculationactivity"]], "Class: SummaryStatisticsReport": [[840, "class-summarystatisticsreport"]], "Class: UngroupedStatistics": [[842, "class-ungroupedstatistics"]], "Slot: acted_on_behalf_of": [[845, "slot-acted-on-behalf-of"]], "Slot: agents": [[846, "slot-agents"]], "Slot: annotation_property_count": [[847, "slot-annotation-property-count"]], "Slot: anonymous_class_expression_count": [[848, "slot-anonymous-class-expression-count"]], "Slot: anonymous_individual_count": [[849, "slot-anonymous-individual-count"]], "Slot: by_category": [[850, "slot-by-category"]], "Slot: by_ontology": [[851, "slot-by-ontology"]], "Slot: by_subset": [[852, "slot-by-subset"]], "Slot: by_taxon": [[853, "slot-by-taxon"]], "Slot: change_summary": [[854, "slot-change-summary"]], "Slot: class_count": [[855, "slot-class-count"]], "Slot: class_count_by_category": [[856, "slot-class-count-by-category"]], "Slot: class_count_by_subset": [[857, "slot-class-count-by-subset"]], "Slot: class_count_excluding_deprecated": [[858, "slot-class-count-excluding-deprecated"]], "Slot: class_count_with_definitions": [[859, "slot-class-count-with-definitions"]], "Slot: class_count_with_text_definitions": [[860, "slot-class-count-with-text-definitions"]], "Slot: class_count_without_text_definitions": [[861, "slot-class-count-without-text-definitions"]], "Slot: class_statistic_group": [[862, "slot-class-statistic-group"]], "Slot: compared_with": [[863, "slot-compared-with"]], "Slot: contributor_id": [[864, "slot-contributor-id"]], "Slot: contributor_name": [[865, "slot-contributor-name"]], "Slot: contributor_summary": [[866, "slot-contributor-summary"]], "Slot: count_statistic": [[867, "slot-count-statistic"]], "Slot: datatype_property_count": [[868, "slot-datatype-property-count"]], "Slot: deprecated_class_count": [[869, "slot-deprecated-class-count"]], "Slot: deprecated_object_property_count": [[870, "slot-deprecated-object-property-count"]], "Slot: description_logic_profile": [[872, "slot-description-logic-profile"]], "Slot: distinct_synonym_count": [[873, "slot-distinct-synonym-count"]], "Slot: edge_count_by_predicate": [[874, "slot-edge-count-by-predicate"]], "Slot: ended_at_time": [[875, "slot-ended-at-time"]], "Slot: entailed_edge_count_by_predicate": [[876, "slot-entailed-edge-count-by-predicate"]], "Slot: equivalent_classes_axiom_count": [[877, "slot-equivalent-classes-axiom-count"]], "Slot: equivalentclasses_axiom_count": [[878, "slot-equivalentclasses-axiom-count"]], "Slot: facet": [[879, "slot-facet"]], "Slot: filtered_count": [[880, "slot-filtered-count"]], "Summary Statistics Datamodel": [[882, "summary-statistics-datamodel"]], "Slot: individual_count": [[883, "slot-individual-count"]], "Slot: individual_statistic_group": [[884, "slot-individual-statistic-group"]], "Slot: mapping_count": [[886, "slot-mapping-count"]], "Slot: mapping_statement_count_by_object_source": [[887, "slot-mapping-statement-count-by-object-source"]], "Slot: mapping_statement_count_by_predicate": [[888, "slot-mapping-statement-count-by-predicate"]], "Slot: mapping_statement_count_subject_by_object_source": [[889, "slot-mapping-statement-count-subject-by-object-source"]], "Slot: merged_class_count": [[890, "slot-merged-class-count"]], "Slot: metadata_statistic_group": [[891, "slot-metadata-statistic-group"]], "Slot: named_individual_count": [[892, "slot-named-individual-count"]], "Slot: non_deprecated_class_count": [[893, "slot-non-deprecated-class-count"]], "Slot: non_deprecated_object_property_count": [[894, "slot-non-deprecated-object-property-count"]], "Slot: normalization_comments": [[895, "slot-normalization-comments"]], "Slot: object_property_count": [[896, "slot-object-property-count"]], "Slot: ontologies": [[897, "slot-ontologies"]], "Slot: ontology_count": [[898, "slot-ontology-count"]], "Slot: owl_axiom_count": [[899, "slot-owl-axiom-count"]], "Slot: owl_statistic_group": [[900, "slot-owl-statistic-group"]], "Slot: partitions": [[901, "slot-partitions"]], "Slot: property_count": [[903, "slot-property-count"]], "Slot: property_statistic_group": [[904, "slot-property-statistic-group"]], "Slot: rdf_triple_count": [[905, "slot-rdf-triple-count"]], "Slot: role_counts": [[906, "slot-role-counts"]], "Slot: started_at_time": [[907, "slot-started-at-time"]], "Slot: subclass_of_axiom_count": [[908, "slot-subclass-of-axiom-count"]], "Slot: subset_count": [[909, "slot-subset-count"]], "summary-statistics": [[910, "summary-statistics"]], "Slot: synonym_statement_count": [[911, "slot-synonym-statement-count"]], "Slot: synonym_statement_count_by_predicate": [[912, "slot-synonym-statement-count-by-predicate"]], "Slot: unsatisfiable_class_count": [[915, "slot-unsatisfiable-class-count"]], "Slot: untyped_entity_count": [[916, "slot-untyped-entity-count"]], "Slot: version_info": [[918, "slot-version-info"]], "Slot: was_associated_with": [[919, "slot-was-associated-with"]], "Slot: was_generated_by": [[920, "slot-was-generated-by"]], "Enum: ConfigurationOption": [[922, "enum-configurationoption"]], "Class: PredicateTerm": [[936, "class-predicateterm"]], "Class: SubjectTerm": [[939, "class-subjectterm"]], "Class: Taxon": [[940, "class-taxon"]], "Class: TaxonConstraint": [[941, "class-taxonconstraint"]], "Slot: asserted": [[946, "slot-asserted"]], "Slot: candidate": [[947, "slot-candidate"]], "Slot: contradicted_by": [[949, "slot-contradicted-by"]], "Slot: evolutionary": [[951, "slot-evolutionary"]], "Taxon Constraints Reporting Datamodel": [[953, "taxon-constraints-reporting-datamodel"]], "Slot: never_in": [[955, "slot-never-in"]], "Slot: only_in": [[956, "slot-only-in"]], "Slot: predicates": [[958, "slot-predicates"]], "Slot: present_in": [[959, "slot-present-in"]], "Slot: present_in_ancestor_of": [[960, "slot-present-in-ancestor-of"]], "Slot: redundant": [[961, "slot-redundant"]], "Slot: redundant_with": [[962, "slot-redundant-with"]], "Slot: redundant_with_only_in": [[963, "slot-redundant-with-only-in"]], "Slot: sources": [[964, "slot-sources"], [1017, "slot-sources"]], "Slot: taxon": [[966, "slot-taxon"]], "Slot: unsatisfiable": [[968, "slot-unsatisfiable"]], "Slot: via_terms": [[969, "slot-via-terms"]], "Class: HasSpan": [[978, "class-hasspan"]], "Class: TextAnnotation": [[988, "class-textannotation"]], "Class: TextAnnotationConfiguration": [[989, "class-textannotationconfiguration"]], "Class: TextAnnotationResultSet": [[990, "class-textannotationresultset"]], "Class: TextualElement": [[991, "class-textualelement"]], "Slot: confidence": [[998, "slot-confidence"], [1063, "slot-confidence"]], "Text Annotator Datamodel": [[1001, "text-annotator-datamodel"]], "Slot: info": [[1002, "slot-info"], [1068, "slot-info"]], "Slot: is_longest_match": [[1003, "slot-is-longest-match"]], "Slot: match_string": [[1005, "slot-match-string"]], "Slot: match_type": [[1006, "slot-match-type"]], "Slot: matches_whole_text": [[1007, "slot-matches-whole-text"]], "Slot: model": [[1008, "slot-model"]], "Slot: object_aliases": [[1009, "slot-object-aliases"]], "Slot: object_categories": [[1010, "slot-object-categories"]], "Slot: parent_document": [[1014, "slot-parent-document"]], "Slot: source_text": [[1016, "slot-source-text"]], "Slot: subject_end": [[1018, "slot-subject-end"]], "Slot: subject_start": [[1021, "slot-subject-start"]], "Slot: subject_text_id": [[1022, "slot-subject-text-id"]], "Slot: text": [[1023, "slot-text"]], "text-annotator": [[1024, "text-annotator"]], "Slot: token_exclusion_list": [[1025, "slot-token-exclusion-list"]], "Class: ConstraintComponent": [[1028, "class-constraintcomponent"]], "Class: ExternalReferenceValidationResult": [[1035, "class-externalreferencevalidationresult"]], "Class: MappingValidationResult": [[1040, "class-mappingvalidationresult"]], "Class: NamedResource": [[1041, "class-namedresource"]], "Class: RepairConfiguration": [[1046, "class-repairconfiguration"]], "Class: RepairOperation": [[1047, "class-repairoperation"]], "Class: RepairReport": [[1048, "class-repairreport"]], "Class: Report": [[1049, "class-report"]], "Class: Result": [[1050, "class-result"]], "Enum: SeverityOptions": [[1051, "enum-severityoptions"]], "Class: TypeSeverityKeyValue": [[1055, "class-typeseveritykeyvalue"]], "Class: ValidationConfiguration": [[1058, "class-validationconfiguration"]], "Class: ValidationReport": [[1059, "class-validationreport"]], "Class: ValidationResult": [[1060, "class-validationresult"]], "Enum: ValidationResultType": [[1061, "enum-validationresulttype"]], "Slot: dry_run": [[1064, "slot-dry-run"]], "Slot: http_response_code": [[1065, "slot-http-response-code"]], "Validation Results Datamodel": [[1067, "validation-results-datamodel"]], "Slot: instantiates": [[1069, "slot-instantiates"]], "Slot: max_number_results_per_type": [[1070, "slot-max-number-results-per-type"]], "Slot: modified": [[1071, "slot-modified"]], "Slot: number_of_attempts": [[1072, "slot-number-of-attempts"]], "Slot: object_info": [[1075, "slot-object-info"]], "Slot: object_str": [[1076, "slot-object-str"]], "Slot: problem": [[1079, "slot-problem"]], "Slot: prompt_info": [[1080, "slot-prompt-info"]], "Slot: repairs": [[1081, "slot-repairs"]], "Slot: schema_path": [[1083, "slot-schema-path"]], "Slot: severity": [[1084, "slot-severity"]], "Slot: subject_info": [[1088, "slot-subject-info"]], "Slot: successful": [[1089, "slot-successful"]], "Slot: suggested_modifications": [[1090, "slot-suggested-modifications"]], "Slot: suggested_predicate": [[1091, "slot-suggested-predicate"]], "Slot: time_checked": [[1092, "slot-time-checked"]], "Slot: type_severity_map": [[1094, "slot-type-severity-map"]], "Slot: validation_configuration": [[1097, "slot-validation-configuration"]], "validaton-results": [[1098, "validaton-results"]], "FAQ: Architecture and Design": [[1099, "faq-architecture-and-design"]], "What is an interface?": [[1099, "what-is-an-interface"]], "What is a Data Model?": [[1099, "what-is-a-data-model"]], "What is an iterator and why does OAK use them so much?": [[1099, "what-is-an-iterator-and-why-does-oak-use-them-so-much"]], "FAQ: Command Line": [[1100, "faq-command-line"]], "How do I see a list of commands?": [[1100, "how-do-i-see-a-list-of-commands"]], "How do I get help on a command?": [[1100, "how-do-i-get-help-on-a-command"]], "How do I get more examples of command line usage?": [[1100, "how-do-i-get-more-examples-of-command-line-usage"]], "I want to query an ontology, what do I pass for the --input option?": [[1100, "i-want-to-query-an-ontology-what-do-i-pass-for-the-input-option"]], "Why do I get a \u201cno such option\u201d error when I pass the \u201c\u2013input\u201d option?": [[1100, "why-do-i-get-a-no-such-option-error-when-i-pass-the-input-option"]], "What do the codes \u201ci\u201d and \u201cp\u201d mean?": [[1100, "what-do-the-codes-i-and-p-mean"]], "Can I pass a list of IDs (CURIEs) as input to a command?": [[1100, "can-i-pass-a-list-of-ids-curies-as-input-to-a-command"]], "Can I pass entity labels as command inputs?": [[1100, "can-i-pass-entity-labels-as-command-inputs"]], "Can I pass lexical queries as command inputs?": [[1100, "can-i-pass-lexical-queries-as-command-inputs"]], "Can I pass the results of graph queries as command inputs?": [[1100, "can-i-pass-the-results-of-graph-queries-as-command-inputs"]], "Can I make boolean combinations of query terms?": [[1100, "can-i-make-boolean-combinations-of-query-terms"]], "Can I chain commands together, unix-style?": [[1100, "can-i-chain-commands-together-unix-style"]], "What does the symbol @ mean in a query term list": [[1100, "what-does-the-symbol-mean-in-a-query-term-list"]], "Can I use the command line to visualize a subgraph?": [[1100, "can-i-use-the-command-line-to-visualize-a-subgraph"]], "Is there an over-arching philosophy or set of design principles to the OAK command line?": [[1100, "is-there-an-over-arching-philosophy-or-set-of-design-principles-to-the-oak-command-line"]], "The command isn\u2019t working the way I expected - how do I get help?": [[1100, "the-command-isn-t-working-the-way-i-expected-how-do-i-get-help"]], "FAQ: Contributing": [[1101, "faq-contributing"]], "How can I contribute?": [[1101, "how-can-i-contribute"]], "How do I stay involved?": [[1101, "how-do-i-stay-involved"]], "FAQ: General": [[1102, "faq-general"]], "What is OAK?": [[1102, "what-is-oak"]], "Are there any tutorials for OAK?": [[1102, "are-there-any-tutorials-for-oak"]], "Are there runnable examples of how to use OAK?": [[1102, "are-there-runnable-examples-of-how-to-use-oak"]], "I am familiar with both Python and Ontologies. Where should I start?": [[1102, "i-am-familiar-with-both-python-and-ontologies-where-should-i-start"]], "I find ontologies confusing. Is there a general guide to help me?": [[1102, "i-find-ontologies-confusing-is-there-a-general-guide-to-help-me"]], "Why is it called OAK?": [[1102, "why-is-it-called-oak"]], "How do I install OAK?": [[1102, "how-do-i-install-oak"]], "Can I use OAK if I don\u2019t know Python?": [[1102, "can-i-use-oak-if-i-don-t-know-python"]], "Can I contribute to OAK?": [[1102, "can-i-contribute-to-oak"]], "Is OAK just for bio-ontologies?": [[1102, "is-oak-just-for-bio-ontologies"]], "Can OAK access ontologies in ontology portals such as MatPortal or BioPortal?": [[1102, "can-oak-access-ontologies-in-ontology-portals-such-as-matportal-or-bioportal"]], "Can OAK access ontologies in triplestores such as OntoBee or Ubergraph?": [[1102, "can-oak-access-ontologies-in-triplestores-such-as-ontobee-or-ubergraph"]], "Can OAK access local files?": [[1102, "can-oak-access-local-files"]], "Can OAK access OBO Format files?": [[1102, "can-oak-access-obo-format-files"]], "Does OAK support all of OWL?": [[1102, "does-oak-support-all-of-owl"]], "Does OAK support reasoning?": [[1102, "does-oak-support-reasoning"]], "Can I use OAK to do graph queries over ontologies?": [[1102, "can-i-use-oak-to-do-graph-queries-over-ontologies"]], "Can I use OAK to do lexical search?": [[1102, "can-i-use-oak-to-do-lexical-search"]], "Can I use OAK as a text annotator?": [[1102, "can-i-use-oak-as-a-text-annotator"]], "FAQ": [[1103, "faq"]], "FAQ: Ontologies": [[1104, "faq-ontologies"]], "What is an ontology?": [[1104, "what-is-an-ontology"]], "Do we need ontologies now we have ChatGPT?": [[1104, "do-we-need-ontologies-now-we-have-chatgpt"]], "What is OWL?": [[1104, "what-is-owl"]], "What is OBO Format?": [[1104, "what-is-obo-format"]], "What is OBO": [[1104, "what-is-obo"]], "What\u2019s a synonym and how do I access them?": [[1104, "what-s-a-synonym-and-how-do-i-access-them"]], "Ancestor statistics": [[1104, "id2"], [1129, "id2"], [1135, "id1"]], "FAQ: Troubleshooting": [[1105, "faq-troubleshooting"]], "Why do I get a \u201cError: No such option: -i\u201d message": [[1105, "why-do-i-get-a-error-no-such-option-i-message"]], "How do I get a BioPortal API key?": [[1105, "how-do-i-get-a-bioportal-api-key"]], "My OBO Format file won\u2019t parse": [[1105, "my-obo-format-file-won-t-parse"]], "My OWL file takes too long to load": [[1105, "my-owl-file-takes-too-long-to-load"]], "My cached SQLite ontology is out of date": [[1105, "my-cached-sqlite-ontology-is-out-of-date"]], "I don\u2019t understand the interface/method I want to use": [[1105, "i-don-t-understand-the-interface-method-i-want-to-use"]], "Glossary": [[1106, "glossary"]], "Aliases and Synonyms": [[1107, "aliases-and-synonyms"]], "Use Cases": [[1107, "use-cases"]], "Search": [[1107, "search"], [1129, "search"], [1149, "search"], [1163, "search"]], "Text mining and NLP": [[1107, "text-mining-and-nlp"]], "Different aliases for different communities": [[1107, "different-aliases-for-different-communities"]], "Different Languages": [[1107, "different-languages"]], "Different approaches to representing synonym metadata": [[1107, "different-approaches-to-representing-synonym-metadata"]], "Representation of synonyms in OAK": [[1107, "representation-of-synonyms-in-oak"]], "Simple Core Model": [[1107, "simple-core-model"]], "HPO basic aliases": [[1107, "id1"]], "Obo Graph Data Model": [[1107, "obo-graph-data-model"]], "HPO full aliases": [[1107, "id2"]], "Associations and Curated Annotations": [[1108, "associations-and-curated-annotations"]], "Background": [[1108, "background"], [1118, "background"]], "Association support in OAK": [[1108, "association-support-in-oak"]], "Data Model": [[1108, "data-model"], [1118, "data-model"], [1171, "data-model"]], "Selecting association sources": [[1108, "selecting-association-sources"]], "Further reading": [[1108, "further-reading"], [1110, "further-reading"], [1113, "further-reading"], [1114, "further-reading"], [1116, "further-reading"], [1118, "further-reading"]], "OAK Basics": [[1109, "oak-basics"]], "What is an ontology and why would I want to access one?": [[1109, "what-is-an-ontology-and-why-would-i-want-to-access-one"]], "Ontology languages, standards, and formats": [[1109, "ontology-languages-standards-and-formats"]], "Core OAK concepts": [[1109, "core-oak-concepts"]], "Identifying entities: CURIEs and URIs": [[1110, "curies-and-uris"]], "Prefix maps": [[1110, "prefix-maps"]], "Querying prefixmaps": [[1110, "querying-prefixmaps"]], "Example prefixes": [[1110, "id1"]], "Non-default prefixmaps": [[1110, "non-default-prefixmaps"]], "Structure of identifiers": [[1110, "structure-of-identifiers"]], "The OAK Guide": [[1111, "the-oak-guide"]], "Learning More": [[1112, "learning-more"]], "Logical Definitions": [[1113, "logical-definitions"]], "Logical Definitions in OWL": [[1113, "logical-definitions-in-owl"]], "Genus-differentia form logical definitions": [[1113, "genus-differentia-form-logical-definitions"]], "The Obo Graphs Model": [[1113, "the-obo-graphs-model"]], "Querying for logical definitions in OAK": [[1113, "querying-for-logical-definitions-in-oak"]], "uberon nail logical definitions": [[1113, "id2"]], "Reasoning using logical definitions": [[1113, "reasoning-using-logical-definitions"]], "Logical definitions and design patterns": [[1113, "logical-definitions-and-design-patterns"]], "Generating logical definitions": [[1113, "generating-logical-definitions"]], "Analyzing logical definitions": [[1113, "analyzing-logical-definitions"]], "Validating logical definitions": [[1113, "validating-logical-definitions"]], "Mappings and Cross-References": [[1114, "mappings-and-cross-references"]], "Mappings in OAK": [[1114, "mappings-in-oak"]], "uberon sssom mappings": [[1114, "id1"]], "In Python": [[1114, "in-python"]], "Generating Mappings": [[1114, "generating-mappings"]], "Obsoletion": [[1115, "obsoletion"]], "Looking up obsoleted entities": [[1115, "looking-up-obsoleted-entities"]], "Conventions and standards": [[1115, "conventions-and-standards"]], "obsolete entities should not be in the signature of any logical axiom": [[1115, "obsolete-entities-should-not-be-in-the-signature-of-any-logical-axiom"]], "obsolete entities should be accompanied by metadata that provides additional context for humans and machines": [[1115, "obsolete-entities-should-be-accompanied-by-metadata-that-provides-additional-context-for-humans-and-machines"]], "Merged entities": [[1115, "merged-entities"]], "Further Reading": [[1115, "further-reading"]], "Primary Labels": [[1116, "primary-labels"]], "Looking up labels": [[1116, "looking-up-labels"]], "Custom label annotation properties": [[1116, "custom-label-annotation-properties"]], "Multilingual ontologies": [[1116, "multilingual-ontologies"]], "Other edge cases": [[1116, "other-edge-cases"]], "Relationships and Graphs": [[1117, "relationships-and-graphs"]], "Exploring relationships": [[1117, "exploring-relationships"]], "Graph Traversal and Relation Graph Reasoning": [[1117, "graph-traversal-and-relation-graph-reasoning"]], "Graph Traversal Strategies": [[1117, "graph-traversal-strategies"]], "Examples of where entailment yields more": [[1117, "examples-of-where-entailment-yields-more"]], "Examples of where graph traversal yields more ancestors than entailment": [[1117, "examples-of-where-graph-traversal-yields-more-ancestors-than-entailment"]], "Which strategy should I use?": [[1117, "which-strategy-should-i-use"]], "A note on entailed direct edges": [[1117, "a-note-on-entailed-direct-edges"]], "Computing Similarity between Entities": [[1118, "computing-similarity-between-entities"]], "Concepts": [[1118, "concepts"]], "Jaccard Similarity": [[1118, "jaccard-similarity"]], "Information Content": [[1118, "information-content"]], "Aggregate measures for comparing entities": [[1118, "aggregate-measures-for-comparing-entities"]], "Vector-based approaches": [[1118, "vector-based-approaches"]], "Implementations": [[1118, "implementations"], [1140, "implementations"], [1152, "implementations"]], "Default Implementation": [[1118, "default-implementation"]], "Ubergraph": [[1118, "ubergraph"], [1131, "ubergraph"]], "Semsimian": [[1118, "semsimian"]], "FHIR Conversions": [[1119, "fhir-conversions"]], "CLI": [[1119, "cli"]], "Config file": [[1119, "config-file"]], "How-To Guides": [[1120, "how-to-guides"]], "How to use Large Language Models (LLMs) with OAK": [[1123, "how-to-use-large-language-models-llms-with-oak"]], "LLM frameworks that use OAK": [[1123, "llm-frameworks-that-use-oak"]], "OntoGPT": [[1123, "ontogpt"]], "CurateGPT": [[1123, "curategpt"]], "Talisman": [[1123, "talisman"]], "Using OAK in conjunction with existing LLM tools": [[1123, "using-oak-in-conjunction-with-existing-llm-tools"]], "OAK LLM Adapter": [[1123, "oak-llm-adapter"]], "Annotation": [[1123, "annotation"], [1151, "annotation"], [1153, "annotation"], [1158, "annotation"]], "Suggesting Definitions": [[1123, "suggesting-definitions"]], "Validating Mappings": [[1123, "validating-mappings"]], "Selecting alternative models": [[1123, "selecting-alternative-models"]], "Installing LLM plugins": [[1123, "installing-llm-plugins"]], "Mixtral via Ollama and LiteLLM": [[1123, "mixtral-via-ollama-and-litellm"]], "Mixtral via groq and LiteLLM": [[1123, "mixtral-via-groq-and-litellm"]], "How to Validate an OBO ontology using Obo Metadata Ontology schema": [[1124, "how-to-validate-an-obo-ontology-using-obo-metadata-ontology-schema"]], "Steps": [[1124, "steps"]], "Step 1: Obtain the sqlite version of the ontology": [[1124, "step-1-obtain-the-sqlite-version-of-the-ontology"]], "Step 2: Install oaklib": [[1124, "step-2-install-oaklib"]], "Step 3: Validate an individual ontology": [[1124, "step-3-validate-an-individual-ontology"]], "Step 3 (alternative): Validate multiple ontologies": [[1124, "step-3-alternative-validate-multiple-ontologies"]], "Caveats": [[1124, "caveats"]], "Using your own schema": [[1124, "using-your-own-schema"]], "How this works": [[1124, "how-this-works"], [1133, "how-this-works"]], "Analysis": [[1124, "analysis"]], "How to write a plugin": [[1126, "how-to-write-a-plugin"]], "What is a plugin?": [[1126, "what-is-a-plugin"]], "An example plugin": [[1126, "an-example-plugin"]], "Creating a plugin": [[1126, "creating-a-plugin"]], "Discuss on the issue tracker": [[1126, "discuss-on-the-issue-tracker"]], "Create a new project": [[1126, "create-a-new-project"], [1130, "create-a-new-project"]], "Implement one or more interfaces": [[1126, "implement-one-or-more-interfaces"]], "Implement a selector": [[1126, "implement-a-selector"]], "Write tests": [[1126, "write-tests"]], "Ontology Access Kit (OAK) Documentation": [[1127, "ontology-access-kit-oak-documentation"]], "Indices and tables": [[1127, "indices-and-tables"]], "Tutorial": [[1128, "tutorial"]], "Part 1: Getting Started": [[1129, "part-1-getting-started"]], "Installation": [[1129, "installation"]], "Install from PyPI": [[1129, "install-from-pypi"]], "Run the OAK command": [[1129, "run-the-oak-command"]], "Basics": [[1129, "basics"]], "Query the OBO Library": [[1129, "query-the-obo-library"]], "Working with local files": [[1129, "working-with-local-files"]], "Introduction to graphs and trees": [[1129, "introduction-to-graphs-and-trees"]], "Fetching ancestors": [[1129, "fetching-ancestors"]], "Predicate Abbreviations": [[1129, "predicate-abbreviations"]], "Ancestor Statistics": [[1129, "ancestor-statistics"]], "Oak Trees": [[1129, "oak-trees"]], "Advanced Search": [[1129, "advanced-search"]], "Using search terms as parameters": [[1129, "using-search-terms-as-parameters"]], "Chaining Commands": [[1129, "chaining-commands"]], "Visualization": [[1129, "visualization"]], "Using other backends": [[1129, "using-other-backends"]], "Using Ubergraph": [[1129, "using-ubergraph"]], "Using Ontobee": [[1129, "using-ontobee"]], "Using BioPortal and OntoPortal": [[1129, "using-bioportal-and-ontoportal"]], "Annotate results": [[1129, "id3"]], "Using OLS": [[1129, "using-ols"]], "OLS SSSOM": [[1129, "id4"]], "Next steps": [[1129, "next-steps"]], "Part 2: Basic Python": [[1130, "part-2-basic-python"]], "Install Poetry": [[1130, "install-poetry"]], "Basic Concepts": [[1130, "basic-concepts"]], "Code the first example": [[1130, "code-the-first-example"]], "Extending the example": [[1130, "extending-the-example"]], "Part 3: Triplestore Backends": [[1131, "part-3-triplestore-backends"]], "Triplestore Concepts": [[1131, "triplestore-concepts"]], "Connecting": [[1131, "connecting"], [1163, "connecting"]], "Basic Operations": [[1131, "basic-operations"]], "Relationships": [[1131, "relationships"]], "Part 4: OboGraphs": [[1132, "part-4-obographs"]], "OboGraphs": [[1132, "obographs"]], "OboGraph Interface": [[1132, "obograph-interface"], [1172, "obograph-interface"]], "Code examples": [[1132, "code-examples"]], "Part 5: Graph Visualization": [[1133, "part-5-graph-visualization"]], "Install Graphviz": [[1133, "install-graphviz"]], "Install OBOGraphViz": [[1133, "install-obographviz"]], "Command Line Usage": [[1133, "command-line-usage"], [1143, "command-line-usage"], [1148, "command-line-usage"]], "Programmatic usage": [[1133, "programmatic-usage"]], "Part 6: Working With OWL": [[1134, "part-6-working-with-owl"]], "OWL Datamodel": [[1134, "owl-datamodel"]], "OwlInterface": [[1134, "owlinterface"]], "ROBOT Plugin": [[1134, "robot-plugin"]], "Part 7: SQLite files": [[1135, "part-7-sqlite-files"]], "Download a SQLite file": [[1135, "download-a-sqlite-file"]], "Example": [[1135, "example"]], "Fetching ready-made SQLite files": [[1135, "fetching-ready-made-sqlite-files"]], "Building your own SQLite files": [[1135, "building-your-own-sqlite-files"]], "With docker": [[1135, "with-docker"]], "Without docker": [[1135, "without-docker"]], "Validating an ontology": [[1135, "validating-an-ontology"]], "Other RDBMSs": [[1135, "other-rdbmss"]], "Python ORM": [[1135, "python-orm"]], "Part 8: Applying Changes to Ontologies": [[1136, "part-8-applying-changes-to-ontologies"]], "About KGCL": [[1136, "about-kgcl"]], "Example: Sqlite3": [[1136, "example-sqlite3"]], "Example: OBO Files": [[1136, "example-obo-files"]], "Introduction": [[1137, "introduction"]], "Basic Python Example": [[1137, "basic-python-example"]], "Basic Command Line Example": [[1137, "basic-command-line-example"]], "Jupyter Notebooks": [[1139, "jupyter-notebooks"]], "Architecture": [[1140, "architecture"]], "Ontology Interfaces": [[1140, "ontology-interfaces"]], "Other Interfaces": [[1140, "other-interfaces"]], "Example: OWL Ontology Interface": [[1140, "example-owl-ontology-interface"]], "Partial and Complete Implementation": [[1140, "partial-and-complete-implementation"]], "Best Practice": [[1141, "best-practice"]], "External Services": [[1141, "external-services"]], "Iterators": [[1141, "iterators"]], "Weaving calls together": [[1141, "weaving-calls-together"]], "Chunking": [[1141, "chunking"]], "Abstract Class": [[1142, "abstract-class"]], "Converters": [[1143, "converters"]], "Converting from Obo Graphs": [[1143, "converting-from-obo-graphs"]], "OBO Graph to CX Converter": [[1144, "obo-graph-to-cx-converter"]], "OBO Graph to FHIR Converter": [[1145, "obo-graph-to-fhir-converter"]], "OBO Graph to OBO Format Converter": [[1146, "obo-graph-to-obo-format-converter"]], "OBO Graph to OWL Converter": [[1147, "obo-graph-to-owl-converter"]], "Aggregator Adapter": [[1148, "aggregator-adapter"]], "Documentation": [[1148, "documentation"], [1156, "documentation"]], "Bioportal Adapter": [[1149, "bioportal-adapter"]], "API Keys": [[1149, "api-keys"]], "Command Line Examples": [[1149, "command-line-examples"], [1151, "command-line-examples"], [1153, "command-line-examples"], [1158, "command-line-examples"]], "Code": [[1149, "code"], [1151, "code"], [1153, "code"], [1154, "code"], [1155, "code"], [1157, "code"], [1158, "code"], [1159, "code"], [1160, "code"], [1161, "code"], [1162, "code"], [1163, "code"]], "FunOwl Adapter": [[1150, "funowl-adapter"]], "Gilda Adapter": [[1151, "gilda-adapter"]], "LLM Adapter": [[1153, "llm-adapter"]], "Validation of Mappings": [[1153, "validation-of-mappings"]], "OBO Graph Adapter": [[1154, "obo-graph-adapter"]], "About": [[1154, "about"], [1157, "about"], [1159, "about"], [1160, "about"], [1163, "about"]], "Initialization": [[1154, "initialization"], [1159, "initialization"], [1160, "initialization"], [1162, "initialization"]], "Ontology Lookup Service (OLS) Adapter": [[1155, "ontology-lookup-service-ols-adapter"]], "Ontobee Adapter": [[1156, "ontobee-adapter"]], "Notes": [[1156, "notes"]], "Owlery Adapter": [[1157, "owlery-adapter"]], "PantherDB Adapter": [[1158, "pantherdb-adapter"]], "Enrichment": [[1158, "enrichment"]], "Mapping": [[1158, "mapping"]], "Pronto / OBO Files Adapter": [[1159, "pronto-obo-files-adapter"]], "Input Selector": [[1159, "input-selector"]], "Simple OBO Adapter": [[1160, "simple-obo-adapter"]], "Sparql Adapter": [[1161, "sparql-adapter"]], "SQL Database Adapter": [[1162, "sql-database-adapter"]], "SQL Alchemy ORM Model": [[1162, "sql-alchemy-orm-model"]], "Ubergraph Adapter": [[1163, "ubergraph-adapter"]], "Interfaces Implemented": [[1163, "interfaces-implemented"]], "OAK Library Documentation": [[1164, "oak-library-documentation"]], "Association Provider Interface": [[1165, "association-provider-interface"]], "Command Line Use": [[1165, "command-line-use"], [1171, "command-line-use"]], "Basic Ontology Interface": [[1166, "basic-ontology-interface"]], "Class Enrichment Calculation Interface": [[1167, "class-enrichment-calculation-interface"]], "Differ Interface": [[1168, "differ-interface"]], "Dumper Interface": [[1169, "dumper-interface"]], "Interfaces": [[1170, "interfaces"]], "Mapping Provider Interface": [[1171, "mapping-provider-interface"]], "OWL Interface": [[1173, "owl-interface"]], "Patcher Interface": [[1174, "patcher-interface"]], "Relation Graph": [[1175, "relation-graph"]], "Search Interface": [[1176, "search-interface"]], "Semantic Similarity Interface": [[1177, "semantic-similarity-interface"]], "Subsetting": [[1178, "subsetting"]], "Summary Statistics": [[1179, "summary-statistics"]], "Text Annotator Interface": [[1180, "text-annotator-interface"]], "Validator Interface": [[1181, "validator-interface"]], "Ontology Adapter Selectors": [[1182, "ontology-adapter-selectors"]], "Syntax": [[1182, "syntax"]], "Schemes": [[1182, "schemes"]], "pronto": [[1182, "pronto"]], "prontolib": [[1182, "prontolib"]], "sqlite": [[1182, "sqlite"]], "obosqlite": [[1182, "obosqlite"]], "ontobee": [[1182, "ontobee"]], "ols": [[1182, "ols"]], "bioportal": [[1182, "bioportal"]], "funowl": [[1182, "funowl"]], "Functions": [[1182, "functions"]], "oaklib.utilities.apikey_manager": [[1183, "module-oaklib.utilities.apikey_manager"]], "oaklib.utilities.graph.networkx_bridge": [[1184, "module-oaklib.utilities.graph.networkx_bridge"]], "Utilities for working with networkx": [[1184, "utilities-for-working-with-networkx"]], "oaklib.utilities.graph.relationship_walker": [[1185, "module-oaklib.utilities.graph.relationship_walker"]], "Utilities for traversing Ontology Graphs": [[1185, "utilities-for-traversing-ontology-graphs"]], "oaklib.utilities.lexical.lexical_indexer": [[1186, "module-oaklib.utilities.lexical.lexical_indexer"]], "Lexical Utilities": [[1186, "lexical-utilities"]], "oaklib.utilities.obograph_utils": [[1187, "module-oaklib.utilities.obograph_utils"]], "Utilities for the OBOGraph Datamodel": [[1187, "utilities-for-the-obograph-datamodel"]], "oaklib.utilities.subsets.slimmer_utils": [[1188, "module-oaklib.utilities.subsets.slimmer_utils"]], "Utilities for working with ontology subsets (slims)": [[1188, "utilities-for-working-with-ontology-subsets-slims"]], "oaklib.utilities.table_filler": [[1189, "module-oaklib.utilities.table_filler"]], "oaklib.utilities.taxon": [[1190, "module-oaklib.utilities.taxon"]], "Utilities": [[1191, "utilities"]], "Layering on RDF/OWL": [[1192, "layering-on-rdf-owl"]], "CURIEs, URIs, and prefixmaps": [[1192, "curies-uris-and-prefixmaps"]], "Relationships between entities": [[1192, "relationships-between-entities"]], "Metadata about entities": [[1192, "metadata-about-entities"]], "Challenges": [[1192, "challenges"]], "OMO": [[1192, "omo"]], "Ontology portals": [[1192, "ontology-portals"]], "OAK Approach": [[1192, "oak-approach"]], "Labels": [[1192, "labels"]], "Obsoletion and obsoletion metadata": [[1192, "obsoletion-and-obsoletion-metadata"]], "Search Syntax": [[1193, "search-syntax"]], "Boolean Combinations": [[1193, "boolean-combinations"]], "Search Datamodel": [[1193, "search-datamodel"]]}, "indexentries": {"--about": [[0, "cmdoption-runoak-axioms-about"]], "--adapter-mapping": [[0, "cmdoption-runoak-validate-mappings-adapter-mapping"]], "--add": [[0, "cmdoption-runoak-a"]], "--add-closure-fields": [[0, "cmdoption-runoak-associations-add-closure-fields"], [0, "cmdoption-runoak-associations-counts-add-closure-fields"]], "--add-labels": [[0, "cmdoption-runoak-lexmatch-add-labels"]], "--add-mrcas": [[0, "cmdoption-runoak-tree-add-mrcas"], [0, "cmdoption-runoak-viz-add-mrcas"]], "--additional-metadata": [[0, "cmdoption-runoak-definitions-additional-metadata"], [0, "cmdoption-runoak-term-metadata-additional-metadata"]], "--all": [[0, "cmdoption-runoak-ontology-metadata-all"], [0, "cmdoption-runoak-ontology-versions-all"], [0, "cmdoption-runoak-taxon-constraints-A"]], "--all-languages": [[0, "cmdoption-runoak-labels-all-languages"]], "--allow-labels": [[0, "cmdoption-runoak-enrichment-allow-labels"]], "--allow-missing": [[0, "cmdoption-runoak-fill-table-allow-missing"]], "--analyze": [[0, "cmdoption-runoak-generate-logical-definitions-analyze"]], "--annotated-roots": [[0, "cmdoption-runoak-roots-A"]], "--apply-patch": [[0, "cmdoption-runoak-generate-definitions-apply-patch"], [0, "cmdoption-runoak-generate-synonyms-apply-patch"], [0, "cmdoption-runoak-synonymize-apply-patch"]], "--association-predicates": [[0, "cmdoption-runoak-associations-association-predicates"], [0, "cmdoption-runoak-associations-counts-association-predicates"], [0, "cmdoption-runoak-associations-matrix-association-predicates"], [0, "cmdoption-runoak-enrichment-association-predicates"]], "--associations": [[0, "cmdoption-runoak-diff-associations-g"], [0, "cmdoption-runoak-g"]], "--associations-type": [[0, "cmdoption-runoak-G"]], "--autolabel": [[0, "cmdoption-runoak-associations-autolabel"], [0, "cmdoption-runoak-associations-counts-autolabel"], [0, "cmdoption-runoak-associations-matrix-autolabel"], [0, "cmdoption-runoak-definitions-autolabel"], [0, "cmdoption-runoak-diff-associations-autolabel"], [0, "cmdoption-runoak-diff-via-mappings-autolabel"], [0, "cmdoption-runoak-disjoints-autolabel"], [0, "cmdoption-runoak-enrichment-autolabel"], [0, "cmdoption-runoak-fill-table-autolabel"], [0, "cmdoption-runoak-generate-disjoints-autolabel"], [0, 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"cmdoption-runoak-diff-change-type"]], "--changes-format": [[0, "cmdoption-runoak-apply-changes-format"]], "--changes-input": [[0, "cmdoption-runoak-apply-changes-input"]], "--changes-output": [[0, "cmdoption-runoak-apply-changes-output"]], "--comment": [[0, "cmdoption-runoak-fill-table-comment"]], "--compare-with": [[0, "cmdoption-runoak-statistics-X"]], "--config-file": [[0, "cmdoption-runoak-dump-c"], [0, "cmdoption-runoak-transform-c"]], "--configuration-file": [[0, "cmdoption-runoak-annotate-C"], [0, "cmdoption-runoak-validate-mappings-C"]], "--configure": [[0, "cmdoption-runoak-paths-C"], [0, "cmdoption-runoak-tree-C"], [0, "cmdoption-runoak-viz-C"]], "--contributor": [[0, "cmdoption-runoak-apply-contributor"]], "--cutoff": [[0, "cmdoption-runoak-enrichment-cutoff"], [0, "cmdoption-runoak-validate-cutoff"], [0, "cmdoption-runoak-validate-multiple-cutoff"]], "--dangling": [[0, "cmdoption-runoak-extract-dangling"]], "--days-old": [[0, "cmdoption-runoak-cache-clear-days-old"]], "--delimiter": [[0, "cmdoption-runoak-fill-table-delimiter"]], "--direct": [[0, "cmdoption-runoak-taxon-constraints-direct"]], "--directed": [[0, "cmdoption-runoak-paths-directed"]], "--direction": [[0, "cmdoption-runoak-relationships-direction"]], "--display": [[0, "cmdoption-runoak-definitions-D"], [0, "cmdoption-runoak-descendants-D"], [0, "cmdoption-runoak-info-D"], [0, "cmdoption-runoak-labels-D"], [0, "cmdoption-runoak-tree-D"]], "--down": [[0, "cmdoption-runoak-tree-down"], [0, "cmdoption-runoak-viz-down"]], "--dry-run": [[0, "cmdoption-runoak-apply-dry-run"], [0, "cmdoption-runoak-lint-dry-run"]], "--endpoint": [[0, "cmdoption-runoak-set-apikey-e"]], "--enforce-canonical-ordering": [[0, "cmdoption-runoak-dump-enforce-canonical-ordering"]], "--ensure-strict-prefixes": [[0, "cmdoption-runoak-lexmatch-ensure-strict-prefixes"]], "--evolution-file": [[0, "cmdoption-runoak-apply-taxon-constraints-E"]], "--exclude-existing": [[0, 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"cmdoption-runoak-descendants-M"], [0, "cmdoption-runoak-taxon-constraints-M"]], "--group-by": [[0, "cmdoption-runoak-associations-counts-group-by"], [0, "cmdoption-runoak-diff-associations-group-by"]], "--group-by-defined-by": [[0, "cmdoption-runoak-diff-group-by-defined-by"], [0, "cmdoption-runoak-statistics-group-by-defined-by"]], "--group-by-obo-namespace": [[0, "cmdoption-runoak-diff-group-by-obo-namespace"], [0, "cmdoption-runoak-statistics-group-by-obo-namespace"]], "--group-by-prefix": [[0, "cmdoption-runoak-diff-group-by-prefix"], [0, "cmdoption-runoak-statistics-group-by-prefix"]], "--group-by-property": [[0, "cmdoption-runoak-diff-group-by-property"], [0, "cmdoption-runoak-statistics-group-by-property"]], "--has-prefix": [[0, "cmdoption-runoak-roots-P"], [0, "cmdoption-runoak-statistics-P"]], "--if-absent": [[0, "cmdoption-runoak-associations-if-absent"], [0, "cmdoption-runoak-definitions-if-absent"], [0, "cmdoption-runoak-labels-if-absent"], [0, "cmdoption-runoak-logical-definitions-if-absent"], [0, "cmdoption-runoak-relationships-if-absent"]], "--ignore-invalid-changes": [[0, "cmdoption-runoak-apply-ignore-invalid-changes"], [0, "cmdoption-runoak-apply-obsolete-ignore-invalid-changes"]], "--import-depth": [[0, "cmdoption-runoak-import-depth"]], "--include-abox": [[0, "cmdoption-runoak-relationships-include-abox"]], "--include-aliases": [[0, "cmdoption-runoak-annotate-include-aliases"]], "--include-entailed": [[0, "cmdoption-runoak-relationships-include-entailed"]], "--include-identity-mappings": [[0, "cmdoption-runoak-diff-via-mappings-include-identity-mappings"]], "--include-merged": [[0, "cmdoption-runoak-obsoletes-include-merged"]], "--include-metadata": [[0, "cmdoption-runoak-extract-include-metadata"], [0, "cmdoption-runoak-relationships-include-metadata"]], "--include-predicates": [[0, "cmdoption-runoak-paths-include-predicates"]], "--include-redundant": [[0, "cmdoption-runoak-taxon-constraints-include-redundant"]], "--include-residuals": [[0, "cmdoption-runoak-statistics-include-residuals"]], "--include-tbox": [[0, "cmdoption-runoak-relationships-include-tbox"]], "--information-content-file": [[0, "cmdoption-runoak-similarity-information-content-file"], [0, "cmdoption-runoak-termset-similarity-information-content-file"]], "--input": [[0, "cmdoption-runoak-i"]], "--input-type": [[0, "cmdoption-runoak-I"]], "--intra": [[0, "cmdoption-runoak-diff-via-mappings-intra"]], "--label-fields": [[0, "cmdoption-runoak-query-L"]], "--lexical-index-file": [[0, "cmdoption-runoak-annotate-L"], [0, "cmdoption-runoak-lexmatch-L"]], "--limit": [[0, "cmdoption-runoak-associations-counts-L"]], "--main-score-field": [[0, "cmdoption-runoak-similarity-main-score-field"]], "--mapper": [[0, "cmdoption-runoak-mappings-mapper"]], "--mapping-input": [[0, "cmdoption-runoak-diff-via-mappings-mapping-input"]], "--maps-to-source": [[0, "cmdoption-runoak-mappings-M"], [0, "cmdoption-runoak-normalize-M"]], "--match-column": [[0, "cmdoption-runoak-annotate-A"]], "--matches-whole-text": [[0, "cmdoption-runoak-annotate-W"]], "--matrix-axes": [[0, "cmdoption-runoak-logical-definitions-matrix-axes"]], "--max-hops": [[0, "cmdoption-runoak-tree-max-hops"], [0, "cmdoption-runoak-viz-max-hops"]], "--merge": [[0, "cmdoption-runoak-merge"]], "--meta": [[0, "cmdoption-runoak-viz-meta"]], "--metamodel-mappings": [[0, "cmdoption-runoak-metamodel-mappings"]], "--min-ancestor-information-content": [[0, "cmdoption-runoak-similarity-min-ancestor-information-content"]], "--min-descendants": [[0, "cmdoption-runoak-generate-disjoints-M"]], "--min-facet-count": [[0, "cmdoption-runoak-associations-counts-min-facet-count"]], "--min-jaccard-similarity": [[0, "cmdoption-runoak-similarity-min-jaccard-similarity"]], "--missing-value-token": [[0, "cmdoption-runoak-fill-table-missing-value-token"]], "--model": [[0, "cmdoption-runoak-annotate-m"]], "--named-classes-only": [[0, "cmdoption-runoak-disjoints-named-classes-only"]], "--named-prefix-map": [[0, "cmdoption-runoak-named-prefix-map"]], "--narrow": [[0, "cmdoption-runoak-paths-narrow"]], "--new-date": [[0, "cmdoption-runoak-diff-associations-new-date"]], "--no-a": [[0, "cmdoption-runoak-roots-A"], [0, "cmdoption-runoak-taxon-constraints-A"]], "--no-w": [[0, "cmdoption-runoak-annotate-W"]], "--no-add-closure-fields": [[0, "cmdoption-runoak-associations-add-closure-fields"], [0, "cmdoption-runoak-associations-counts-add-closure-fields"]], "--no-add-labels": [[0, "cmdoption-runoak-lexmatch-add-labels"]], "--no-add-mrcas": [[0, "cmdoption-runoak-tree-add-mrcas"], [0, "cmdoption-runoak-viz-add-mrcas"]], "--no-additional-metadata": [[0, "cmdoption-runoak-definitions-additional-metadata"], [0, "cmdoption-runoak-term-metadata-additional-metadata"]], "--no-all": [[0, "cmdoption-runoak-ontology-metadata-all"], [0, "cmdoption-runoak-ontology-versions-all"], [0, "cmdoption-runoak-taxon-constraints-A"]], "--no-all-languages": [[0, "cmdoption-runoak-labels-all-languages"]], "--no-allow-labels": [[0, "cmdoption-runoak-enrichment-allow-labels"]], "--no-allow-missing": [[0, "cmdoption-runoak-fill-table-allow-missing"]], "--no-analyze": [[0, "cmdoption-runoak-generate-logical-definitions-analyze"]], "--no-annotated-roots": [[0, "cmdoption-runoak-roots-A"]], "--no-apply-patch": [[0, "cmdoption-runoak-generate-definitions-apply-patch"], [0, "cmdoption-runoak-generate-synonyms-apply-patch"], [0, "cmdoption-runoak-synonymize-apply-patch"]], "--no-autolabel": [[0, "cmdoption-runoak-associations-autolabel"], [0, "cmdoption-runoak-associations-counts-autolabel"], [0, "cmdoption-runoak-associations-matrix-autolabel"], [0, "cmdoption-runoak-definitions-autolabel"], [0, "cmdoption-runoak-diff-associations-autolabel"], [0, "cmdoption-runoak-diff-via-mappings-autolabel"], [0, "cmdoption-runoak-disjoints-autolabel"], [0, "cmdoption-runoak-enrichment-autolabel"], [0, "cmdoption-runoak-fill-table-autolabel"], [0, "cmdoption-runoak-generate-disjoints-autolabel"], [0, "cmdoption-runoak-generate-logical-definitions-autolabel"], [0, "cmdoption-runoak-logical-definitions-autolabel"], [0, "cmdoption-runoak-mappings-autolabel"], [0, "cmdoption-runoak-normalize-autolabel"], [0, "cmdoption-runoak-paths-autolabel"], [0, "cmdoption-runoak-query-autolabel"], [0, "cmdoption-runoak-relationships-autolabel"], [0, "cmdoption-runoak-rollup-autolabel"], [0, "cmdoption-runoak-search-autolabel"], [0, "cmdoption-runoak-similarity-autolabel"], [0, "cmdoption-runoak-similarity-pair-autolabel"], [0, "cmdoption-runoak-termset-similarity-autolabel"], [0, "cmdoption-runoak-validate-mappings-autolabel"]], "--no-autosave": [[0, "cmdoption-runoak-autosave"]], "--no-bidirectional": [[0, "cmdoption-runoak-diff-via-mappings-bidirectional"]], "--no-dangling": [[0, "cmdoption-runoak-extract-dangling"]], "--no-direct": [[0, "cmdoption-runoak-taxon-constraints-direct"]], "--no-directed": [[0, "cmdoption-runoak-paths-directed"]], "--no-down": [[0, "cmdoption-runoak-tree-down"], [0, "cmdoption-runoak-viz-down"]], "--no-dry-run": [[0, "cmdoption-runoak-apply-dry-run"], [0, "cmdoption-runoak-lint-dry-run"]], "--no-enforce-canonical-ordering": [[0, "cmdoption-runoak-dump-enforce-canonical-ordering"]], "--no-ensure-strict-prefixes": [[0, "cmdoption-runoak-lexmatch-ensure-strict-prefixes"]], "--no-exclude-existing": [[0, "cmdoption-runoak-generate-disjoints-exclude-existing"]], "--no-expand": [[0, "cmdoption-runoak-apply-expand"], [0, "cmdoption-runoak-apply-obsolete-expand"]], "--no-fill": [[0, "cmdoption-runoak-generate-logical-definitions-fill"]], "--no-filter-category-identical": [[0, "cmdoption-runoak-diff-via-mappings-filter-category-identical"]], "--no-filter-obsoletes": [[0, "cmdoption-runoak-leafs-filter-obsoletes"], [0, "cmdoption-runoak-singletons-filter-obsoletes"], [0, "cmdoption-runoak-terms-filter-obsoletes"]], "--no-filter-redundant": [[0, "cmdoption-runoak-enrichment-filter-redundant"]], "--no-gap-fill": [[0, "cmdoption-runoak-tree-gap-fill"], [0, "cmdoption-runoak-viz-gap-fill"]], "--no-group-by-defined-by": [[0, "cmdoption-runoak-diff-group-by-defined-by"], [0, "cmdoption-runoak-statistics-group-by-defined-by"]], "--no-group-by-obo-namespace": [[0, "cmdoption-runoak-diff-group-by-obo-namespace"], [0, "cmdoption-runoak-statistics-group-by-obo-namespace"]], "--no-group-by-prefix": [[0, "cmdoption-runoak-diff-group-by-prefix"], [0, "cmdoption-runoak-statistics-group-by-prefix"]], "--no-ignore-invalid-changes": [[0, "cmdoption-runoak-apply-ignore-invalid-changes"], [0, "cmdoption-runoak-apply-obsolete-ignore-invalid-changes"]], "--no-include-abox": [[0, "cmdoption-runoak-relationships-include-abox"]], "--no-include-aliases": [[0, "cmdoption-runoak-annotate-include-aliases"]], "--no-include-entailed": [[0, "cmdoption-runoak-relationships-include-entailed"]], "--no-include-identity-mappings": [[0, "cmdoption-runoak-diff-via-mappings-include-identity-mappings"]], "--no-include-merged": [[0, "cmdoption-runoak-obsoletes-include-merged"]], "--no-include-metadata": [[0, "cmdoption-runoak-extract-include-metadata"], [0, "cmdoption-runoak-relationships-include-metadata"]], "--no-include-predicates": [[0, "cmdoption-runoak-paths-include-predicates"]], "--no-include-redundant": [[0, "cmdoption-runoak-taxon-constraints-include-redundant"]], "--no-include-residuals": [[0, "cmdoption-runoak-statistics-include-residuals"]], "--no-include-tbox": [[0, "cmdoption-runoak-relationships-include-tbox"]], "--no-intra": [[0, "cmdoption-runoak-diff-via-mappings-intra"]], "--no-matches-whole-text": [[0, "cmdoption-runoak-annotate-W"]], "--no-merge": [[0, "cmdoption-runoak-merge"]], "--no-meta": [[0, "cmdoption-runoak-viz-meta"]], "--no-named-classes-only": [[0, "cmdoption-runoak-disjoints-named-classes-only"]], "--no-narrow": [[0, "cmdoption-runoak-paths-narrow"]], "--no-obo-model": [[0, "cmdoption-runoak-aliases-obo-model"]], "--no-ontology-only": [[0, 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"keyval": [[0, "cmdoption-runoak-set-apikey-arg-KEYVAL"]], "ontologies": [[0, "cmdoption-runoak-ontology-metadata-arg-ONTOLOGIES"], [0, "cmdoption-runoak-ontology-versions-arg-ONTOLOGIES"]], "subsets": [[0, "cmdoption-runoak-expand-subsets-arg-SUBSETS"]], "table_file": [[0, "cmdoption-runoak-fill-table-arg-TABLE_FILE"]], "terms": [[0, "cmdoption-runoak-aliases-arg-TERMS"], [0, "cmdoption-runoak-ancestors-arg-TERMS"], [0, "cmdoption-runoak-apply-obsolete-arg-TERMS"], [0, "cmdoption-runoak-associations-arg-TERMS"], [0, "cmdoption-runoak-associations-counts-arg-TERMS"], [0, "cmdoption-runoak-associations-matrix-arg-TERMS"], [0, "cmdoption-runoak-axioms-arg-TERMS"], [0, "cmdoption-runoak-definitions-arg-TERMS"], [0, "cmdoption-runoak-descendants-arg-TERMS"], [0, "cmdoption-runoak-diff-terms-arg-TERMS"], [0, "cmdoption-runoak-diff-via-mappings-arg-TERMS"], [0, "cmdoption-runoak-disjoints-arg-TERMS"], [0, "cmdoption-runoak-dump-arg-TERMS"], [0, "cmdoption-runoak-enrichment-arg-TERMS"], [0, 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