Merge pull request #100 from Cellular-Semantics/docs/update-summary-17099859800

docs: update CL_KG summary report

Author: ubyndr

docs/reports/clkg-summary.md

@@ -2,7 +2,7 @@
 
 # CL_KG Summary Report
 
-_Generated: 2025-08-20 12:51 UTC_
+_Generated: 2025-08-20 13:28 UTC_
 
 ---
 

docs/reports/sections/01-global-totals.md

@@ -0,0 +1,9 @@
+# 01 — Global totals
+
+<sub><em>Source: 01_totals.cypher</em></sub>
+
+
+| nodes | relationships |
+| --- | --- |
+| 277146 | 1243035 |
+

docs/reports/sections/02-counts-by-key-label.md

@@ -0,0 +1,20 @@
+# 02 — Counts by key label
+
+<sub><em>Source: 02_counts_by_label.cypher</em></sub>
+
+
+| label | n |
+| --- | --- |
+| Protein | 30972 |
+| Biological_process | 25964 |
+| Disease | 25804 |
+| Cell_cluster | 24850 |
+| Gene | 17532 |
+| Cell | 10888 |
+| Multicellular_anatomical_structure | 10520 |
+| Cellular_component | 4058 |
+| Race | 927 |
+| Developmental_stage | 437 |
+| Dataset | 178 |
+| Assay | 14 |
+

docs/reports/sections/03-average-degree-by-label.md

@@ -0,0 +1,15 @@
+# 03 — Average degree by label
+
+<sub><em>Source: 03_avg_degree_by_label.cypher</em></sub>
+
+
+| label | avg_degree |
+| --- | --- |
+| Dataset | 90.09 |
+| Cellular_component | 15.91 |
+| Cell_cluster | 15.71 |
+| Cell | 13.07 |
+| Protein | 8.87 |
+| Gene | 8.66 |
+| Biological_process | 7.56 |
+

docs/reports/sections/04-relationship-types-by-count.md

@@ -0,0 +1,304 @@
+# 04 — Relationship types by count
+
+<sub><em>Source: 04_relationship_types_count.cypher</em></sub>
+
+
+| rt | c |
+| --- | --- |
+| SUBCLASSOF | 611248 |
+| in_subset | 260582 |
+| development_stage | 217070 |
+| INSTANCEOF | 148096 |
+| has_marker | 108116 |
+| tissue | 93572 |
+| in_taxon | 91611 |
+| has_part | 82917 |
+| located_in | 53728 |
+| sex | 53666 |
+| ncbitaxon_has_rank | 48866 |
+| subcluster_of | 48330 |
+| part_of | 46294 |
+| self_reported_ethnicity | 46286 |
+| involved_in | 44794 |
+| has_participant | 43112 |
+| assay | 39084 |
+| disease | 37642 |
+| has_source | 31364 |
+| never_in_taxon | 27254 |
+| has_marker_set | 26544 |
+| acts_upstream_of_or_within | 24542 |
+| is_active_in | 23242 |
+| has_role | 20930 |
+| produces | 20912 |
+| term_replaced_by | 16199 |
+| exemplar_data_of | 15794 |
+| has_exemplar_data | 15256 |
+| chebi_is_conjugate_base_of | 12140 |
+| chebi_is_conjugate_acid_of | 12140 |
+| has_obsolescence_reason | 11704 |
+| chebi_has_functional_parent | 10980 |
+| has_primary_input | 10158 |
+| composed_primarily_of | 7054 |
+| excluded_subClassOf | 6778 |
+| present_in_taxon | 6712 |
+| consider | 6606 |
+| expresses | 6570 |
+| regulates | 6286 |
+| enables | 6222 |
+| positively_regulates | 5530 |
+| negatively_regulates | 5458 |
+| develops_from | 3768 |
+| acts_upstream_of | 3350 |
+| crossSpeciesExactMatch | 2842 |
+| has_primary_output | 2822 |
+| has_characterizing_marker_set | 2746 |
+| chebi_is_tautomer_of | 2704 |
+| contributor | 2670 |
+| has_primary_input_or_output | 2532 |
+| chebi_is_enantiomer_of | 2508 |
+| capable_of | 2174 |
+| obsolete_some_soma_located_in | 1590 |
+| mutually_spatially_disjoint_with | 1588 |
+| results_in_development_of | 1540 |
+| Population_group | 1408 |
+| hasCountryOfOrigin | 1382 |
+| creator | 1328 |
+| contributes_to_morphology_of | 1264 |
+| has_plasma_membrane_part | 1204 |
+| connects | 1114 |
+| lacks_plasma_membrane_part | 1080 |
+| has_target_end_location | 1038 |
+| occurs_in | 1032 |
+| chebi_has_parent_hydride | 942 |
+| only_in_taxon | 926 |
+| capable_of_part_of | 864 |
+| is_opposite_of | 850 |
+| has_soma_location | 846 |
+| adjacent_to | 810 |
+| results_in_morphogenesis_of | 786 |
+| overlaps | 778 |
+| colocalizes_with | 726 |
+| immediately_preceded_by | 712 |
+| chebi_is_substituent_group_from | 688 |
+| results_in_acquisition_of_features_of | 670 |
+| in_historical_homology_relationship_with | 660 |
+| results_in_assembly_of | 654 |
+| has_target_start_location | 598 |
+| results_in_transport_across | 524 |
+| connected_to | 460 |
+| has_muscle_insertion | 458 |
+| isDemonymOf | 456 |
+| some_soma_located_in | 452 |
+| has_muscle_origin | 438 |
+| results_in_formation_of | 432 |
+| term_editor | 416 |
+| has_potential_to_develop_into | 396 |
+| results_in_organization_of | 394 |
+| vessel_supplies_blood_to | 376 |
+| attached_to | 346 |
+| bounding_layer_of | 336 |
+| bearer_of | 324 |
+| connecting_branch_of | 297 |
+| tributary_of | 290 |
+| innervated_by | 288 |
+| output_of | 278 |
+| BSPO_0000126 | 274 |
+| extends_fibers_into | 270 |
+| partially_overlaps | 268 |
+| continuous_with | 262 |
+| has_quality | 254 |
+| vessel_drains_blood_from | 254 |
+| innervates | 238 |
+| has_synaptic_IO_in_region | 234 |
+| has_high_plasma_membrane_amount | 226 |
+| increased_in_magnitude_relative_to | 224 |
+| decreased_in_magnitude_relative_to | 222 |
+| process_has_causal_agent | 220 |
+| has_low_plasma_membrane_amount | 220 |
+| results_in_movement_of | 214 |
+| has_developmental_contribution_from | 204 |
+| surrounds | 190 |
+| BSPO_0000120 | 184 |
+| has_curation_status | 181 |
+| has_relative_magnitude | 180 |
+| acts_on_population_of | 178 |
+| luminal_space_of | 178 |
+| branching_part_of | 176 |
+| BSPO_0000121 | 172 |
+| has_intermediate | 168 |
+| starts_with | 164 |
+| has_skeleton | 158 |
+| regulates_characteristic | 154 |
+| results_in_maturation_of | 154 |
+| directly_negatively_regulates | 148 |
+| regulates_levels_of | 146 |
+| skeleton_of | 142 |
+| immediate_transformation_of | 142 |
+| results_in_disassembly_of | 140 |
+| negatively_regulates_in_another_organism | 138 |
+| derived_from_ancestral_fusion_of | 134 |
+| results_in_commitment_to | 124 |
+| directly_positively_regulates | 122 |
+| created_by | 118 |
+| proximally_connected_to | 118 |
+| participates_in | 114 |
+| regulates_in_another_organism | 112 |
+| conduit_for | 110 |
+| produced_by | 108 |
+| results_in_transport_along | 98 |
+| directly_regulates | 98 |
+| transformation_of | 94 |
+| has_muscle_antagonist | 94 |
+| dubious_for_taxon | 86 |
+| BSPO_0001107 | 80 |
+| ends_with | 78 |
+| results_in_fusion_of | 78 |
+| contributes_to | 78 |
+| results_in_structural_organization_of | 74 |
+| channel_for | 72 |
+| existence_ends_during | 70 |
+| surrounded_by | 70 |
+| distally_connected_to | 70 |
+| results_in_specification_of | 68 |
+| temporal_interpretation | 64 |
+| results_in_growth_of | 56 |
+| acts_upstream_of4_positive_effect | 54 |
+| BSPO_0005001 | 54 |
+| acts_upstream_of_or_within4_positive_effect | 52 |
+| has_start_location | 52 |
+| channels_from | 52 |
+| results_in_determination_of | 50 |
+| preceded_by | 50 |
+| contains_process | 48 |
+| has_small_molecule_activator | 48 |
+| positively_regulates_in_another_organism | 46 |
+| has_end_location | 46 |
+| results_in_transport_to_from_or_in | 46 |
+| lacks_part | 44 |
+| anteriorly_connected_to | 44 |
+| develops_into | 38 |
+| developmentally_induced_by | 38 |
+| location_of | 38 |
+| subdivision_of | 38 |
+| has_member | 38 |
+| includedInDataCatalog | 38 |
+| channels_into | 36 |
+| positively_regulates_characteristic | 34 |
+| happens_during | 34 |
+| negatively_regulates_characteristic | 34 |
+| synapsed_to | 34 |
+| BSPO_0000122 | 32 |
+| has_not_completed | 30 |
+| existence_starts_and_ends_during | 30 |
+| existence_starts_during | 30 |
+| BSPO_0000123 | 30 |
+| derives_from | 28 |
+| BSPO_0000098 | 28 |
+| BSPO_0000108 | 28 |
+| site_of | 26 |
+| results_in_maintenance_of | 26 |
+| has_stage_marker | 26 |
+| has_potential_to_developmentally_contribute_to | 26 |
+| axon_synapses_in | 26 |
+| has_component | 26 |
+| BSPO_0015014 | 26 |
+| mmusdv_has_stage_marker | 24 |
+| BSPO_0000096 | 24 |
+| BSPO_0000102 | 24 |
+| BSPO_0000107 | 24 |
+| sexually_homologous_to | 24 |
+| simultaneous_with | 22 |
+| directly_develops_from | 22 |
+| BSPO_0001113 | 22 |
+| is_count_of | 20 |
+| acts_upstream_of4_negative_effect | 20 |
+| results_in_remodeling_of | 20 |
+| see_also | 18 |
+| preceding_element_is | 18 |
+| is_homeomorphic_for | 18 |
+| results_in_fission_of | 18 |
+| synapsed_by | 18 |
+| develops_in | 18 |
+| BSPO_0000099 | 18 |
+| protects | 18 |
+| is_positive_form_of | 16 |
+| is_negative_form_of | 16 |
+| acts_upstream_of_or_within4_negative_effect | 16 |
+| results_in | 16 |
+| regulated_by | 16 |
+| developmentally_replaces | 16 |
+| BSPO_0001106 | 16 |
+| BSPO_0001100 | 14 |
+| BSPO_0020001 | 14 |
+| reciprocal_of | 14 |
+| results_in_distribution_of | 12 |
+| confers_advantage_in | 12 |
+| BSPO_0015101 | 12 |
+| existence_starts_with | 12 |
+| BSPO_0001101 | 12 |
+| towards | 12 |
+| http___purl_org_dc_terms_contributor | 12 |
+| BSPO_0015102 | 10 |
+| has_small_molecule_regulator | 10 |
+| existence_ends_with | 10 |
+| BSPO_0001108 | 10 |
+| BSPO_0001115 | 10 |
+| develops_from_part_of | 10 |
+| has_cross_section | 10 |
+| is_direct_form_of | 10 |
+| precedes | 8 |
+| immediately_precedes | 8 |
+| functionally_related_to | 8 |
+| coincident_with | 8 |
+| BSPO_0000100 | 8 |
+| ambiguous_for_taxon | 8 |
+| anastomoses_with | 8 |
+| filtered_through | 8 |
+| in_innermost_side_of | 8 |
+| in_outermost_side_of | 8 |
+| attached_to_part_of | 8 |
+| indirectly_supplies | 8 |
+| nominally_disjoint_with | 6 |
+| has_synaptic_terminal_in | 6 |
+| starts | 6 |
+| realizes | 6 |
+| hasAncestryStatus | 6 |
+| serially_homologous_to | 6 |
+| results_in_developmental_progression_of | 4 |
+| immediately_causally_upstream_of | 4 |
+| results_in_changes_to_anatomical_or_cellular_structure | 4 |
+| directly_develops_into | 4 |
+| pr_has_constituent_monomer | 4 |
+| member_of | 4 |
+| has_no_connections_with | 4 |
+| ends | 4 |
+| characteristic_of | 4 |
+| BSPO_0000097 | 4 |
+| lumen_of | 4 |
+| BSPO_0000124 | 4 |
+| BSPO_0000125 | 4 |
+| is_indirect_form_of | 4 |
+| has_scope | 2 |
+| capable_of_regulating | 2 |
+| ends_during | 2 |
+| involved_in_regulation_of | 2 |
+| has_potential_to_directly_develop_into | 2 |
+| has_sensory_dendrite_in | 2 |
+| has_presynaptic_terminal_in | 2 |
+| has_dendrite_location | 2 |
+| fasciculates_with | 2 |
+| correlated_with | 2 |
+| non_functional_homolog_of | 2 |
+| pr_has_gene_template | 2 |
+| BSPO_0015202 | 2 |
+| BSPO_0015009 | 2 |
+| BSPO_0015012 | 2 |
+| input_of | 2 |
+| existence_ends_during_or_before | 2 |
+| has_2D_boundary | 2 |
+| existence_starts_during_or_after | 2 |
+| posteriorly_connected_to | 2 |
+| trunk_part_of | 2 |
+| layer_part_of | 2 |
+| definition_source | 2 |
+

docs/reports/sections/05-top-tissues-across-clusters.md

@@ -0,0 +1,28 @@
+# 05 — Top tissues across clusters
+
+<sub><em>Source: 05_top_tissues.cypher</em></sub>
+
+
+| tissue | clusters |
+| --- | --- |
+| primary motor cortex | 2308 |
+| hypothalamus | 2179 |
+| primary visual cortex | 1586 |
+| primary somatosensory cortex | 1459 |
+| hippocampal formation | 1201 |
+| anterior cingulate cortex | 1198 |
+| cerebellum | 1160 |
+| brain | 1131 |
+| white matter | 1075 |
+| primary auditory cortex | 1074 |
+| dorsolateral prefrontal cortex | 1004 |
+| midbrain | 975 |
+| middle temporal gyrus | 952 |
+| striatum | 948 |
+| hindbrain | 892 |
+| neocortex | 810 |
+| pallidum | 791 |
+| blood | 725 |
+| ventricular system of brain | 724 |
+| thalamic complex | 650 |
+