Proto-OKN Crosswalk Inventory

Verified 2026-11-09claude-opus-4-8apps.okn.us/federation/sparql

All 269 precomputed cross-KG crosswalks (verified through 2026-11-09), grouped by domain. Each shows the knowledge graphs joined, the shared identifier, the verified overlap count, and example questions the join answers. Every question links to the transcript of the worked example that answers it — the federated SPARQL, the rows it returned, and the reading.

Anatomy & Cell Type

KGsShared keyCountExamples
biomarkerkg ↔ gene-expression-atlas-oknCL8Which immune/blood cell types are used as biomarkers in BiomarkerKB and also assayed at single-cell resolution in GXA?

For a cell type GXA profiles at single-cell resolution (CL), is it used as a clinical biomarker in BiomarkerKB, and for what biomarker readout?
biomarkerkg ↔ proknCL3For an immune cell type used as a biomarker in BiomarkerKB, what tissue-specific marker genes does ProKN record (HuBMAP)?

For a cell type ProKN records tissue-specific marker genes for (CL), is that same cell type used as a biomarker in BiomarkerKB, and do its ProKN markers suggest the biomarker's molecular basis?
gene-expression-atlas-okn ↔ proknCL31For a cell type GXA has single-cell expression for (CL), what marker genes / proteins does ProKN record for that same cell type?

Given ProKN's HuBMAP marker genes for a cell type (CL), does GXA single-cell expression corroborate those genes as enriched in the same cell type?
spoke-genelab ↔ gene-expression-atlas-oknCL4For a cell type examined in a NASA GeneLab spaceflight assay (spoke-genelab, CL), what terrestrial single-cell expression data does GXA hold for the same cell type?

How many of the cell types GXA profiles at single-cell resolution (CL) were also examined in a NASA GeneLab spaceflight assay, and which specific cell types are they?
spoke-genelab ↔ proknCL1For a cell type examined in a NASA GeneLab spaceflight assay (spoke-genelab, CL), what marker genes/proteins does ProKN record for that same cell type?

Which single cell type (CL) is both examined in a GeneLab spaceflight assay and cataloged with ProKN HuBMAP marker genes, and what are those marker genes?
bio101 → ubergraph → biobricks-aopwikiCL (bio101 label)24For the cell types KB Bio 101 describes, how many AOP-Wiki key events are set in the matching Cell Ontology cell-type context, or act on that cell type as their biological object, and how many adverse outcome pathways do they belong to? Rank the bridged cell types.

Among the cells KB Bio 101 itself classifies as reproductive cells (under aura:Reproductive-Cell), which reach AOP-Wiki, which key events involve them, and which adverse outcomes do the pathways through those key events end in?
bio101 → ubergraph → gene-expression-atlas-oknCL (bio101 label)35Which textbook cell types in KB Bio 101 (macrophage, neutrophil, fibroblast, oocyte, ...) are profiled by Expression Atlas, and in how many studies and contrasts each?

For the macrophage, what does KB Bio 101 say its functions are, and which Expression Atlas contrasts profile macrophages? In one contrast that tests the textbook role directly, which genes are most strongly induced?
bio101 → ubergraph → proknCL (bio101 label)13For the cell types KB Bio 101 teaches, which does ProKN describe, with how many marker genes in heart, kidney and liver, and how many metabolites? Rank them.

Which marker genes does ProKN list for each textbook cell type in each organ, and do they include the markers a textbook would name (hemoglobin for red blood cells, immunoglobulin for plasma cells, CD163 / MRC1 for macrophages, KIT and tryptase for mast cells, myelin genes for Schwann cells)?
bio101 → ubergraph → gene-expression-atlas-oknPO (bio101 label)30Which plant organs and tissues KB Bio 101 teaches are sampled in Expression Atlas differential-expression contrasts, in how many contrasts and experiments? Rank them.

When an Expression Atlas contrast samples a plant part KB Bio 101 teaches and is enriched for a process or structure KB Bio 101 teaches, which textbook plant part × textbook process pairs occur in the most contrasts?
biomarkerkg ↔ gene-expression-atlas-oknUBERON27For the tissue a biomarker is sampled from, what baseline and differential expression does GXA report in that same tissue?

How many BiomarkerKG sample-source tissues are covered by a GXA assay?
spoke-genelab ↔ gene-expression-atlas-oknUBERON27For an anatomical entity assayed in NASA GeneLab spaceflight studies (spoke-genelab Anatomy, UBERON), what terrestrial differential-expression data does GXA hold for the same tissue?

For a tissue GXA holds terrestrial differential-expression data on (UBERON), was that same anatomical entity ever assayed in a NASA GeneLab spaceflight study, enabling a microgravity-vs-ground expression comparison?
bio101 → ubergraph → biobricks-aopwikiUBERON (bio101 label)48For the organs and tissues KB Bio 101 describes, how many AOP-Wiki key events are set in the matching UBERON organ context, or act on it as their biological object, and how many adverse outcome pathways do those key events belong to? Rank the bridged anatomy.

What does KB Bio 101 say the thyroid gland does, and which AOP-Wiki key events are set in the thyroid? Which adverse outcome pathways run through them, and what outcomes do those pathways end in?
bio101 → ubergraph → biomarkerkgUBERON (bio101 label)31Which of the organs, tissues and body fluids KB Bio 101 describes are used as the specimen (obo:OBCI_1000018) for BiomarkerKB biomarker assessments, how many assessments each, and of which kind? Rank the bridged anatomy.

When a BiomarkerKB assessment both names a disease KB Bio 101 teaches and is measured in a body part or fluid KB Bio 101 teaches, which textbook disease–specimen pairs occur, and how often? What does that say about where each disease is diagnosed from?
bio101 → ubergraph → gene-expression-atlas-oknUBERON (bio101 label)105For the organs KB Bio 101 describes (heart, liver, kidney, pancreas, ...), how many Expression Atlas differential-expression contrasts and studies are anchored on the matching UBERON tissue? Rank the bridged organs.

What does KB Bio 101 say the liver is made of and does, side by side with the Expression Atlas studies that profile liver tissue, and which of the textbook's liver functions does GXA actually have perturbation experiments for?
bio101 → ubergraph → proknUBERON (bio101 label)54For the organs, tissues and fluids KB Bio 101 describes, how many metabolites does ProKN record each producing, and which of them carry GTEx expression records (and for how many Ensembl genes)? Rank them, and say which textbook anatomy is covered by both sources.

Which metabolites does ProKN record as produced by the widest range of the tissues and fluids KB Bio 101 teaches? List the 30 most widely shared, with the textbook tissues they occur in.
bio101 → ubergraph → spoke-genelabUBERON (bio101 label)17Which organs and tissues KB Bio 101 teaches have been assayed in NASA OSDR spaceflight omics, in how many assays, studies and missions, and in which organisms? Rank them.

For the organs and tissues KB Bio 101 teaches, how many spoke-genelab assays directly compare spaceflight samples with ground-control samples, in which organisms, and on which missions? Rank them.
biohealth → ubergraph → gene-expression-atlas-oknUMLS↔UBERON249For a tissue/organ GXA profiles expression in (UBERON), what does biohealth know about that anatomical entity (UMLS CUI) and its disease/SDoH associations, bridged through ubergraph UMLS->UBERON?

Across anatomical entities biohealth ties to a disease or social-determinant burden (UMLS CUI), how many map through ubergraph to a UBERON tissue that GXA actually profiles expression for?
biohealth → ubergraph → spoke-genelabUMLS↔UBERON35For a tissue/organ a NASA GeneLab spaceflight assay examined (spoke-genelab Anatomy, UBERON), what does biohealth know about that anatomical entity (UMLS CUI), bridged through ubergraph UMLS->UBERON?

Of the 35 anatomical entities biohealth characterizes (UMLS CUI), which were targeted by NASA GeneLab spaceflight assays (spoke-genelab UBERON), and does biohealth flag any of those tissues with disease/SDoH risk relevant to astronaut health?

Biology concepts

KGsShared keyCountExamples
bio101 ↔ biohealthconcept label (bio101 concept name ↔ UMLS concept name)1,213For cellular processes that KB Bio 101 teaches (apoptosis, autophagy, glycolysis, oxidative phosphorylation, phagocytosis, DNA repair, protein folding, DNA methylation), which diseases does BioHealthKG's literature graph link the matching UMLS concept to, and which diseases are linked to all of them?

Across KB Bio 101's textbook concepts, which categories (chemicals, anatomy, physiological processes, organisms, ...) land most often on a type-consistent BioHealthKG concept, and which bridged concepts are the best connected in BioHealthKG's literature graph?

Chemicals

KGsShared keyCountExamples
biobricks-aopwiki ↔ biobricks-tox21CAS285Which Adverse Outcome Pathways have the most chemical stressors that were screened in Tox21, joined on the CAS number?

Same crosswalk, coverage angle: how many AOP-Wiki chemicals are Tox21 chemicals, and how many AOPs have at least one Tox21-screened stressor?
biobricks-aopwiki ↔ biobricks-toxcastCAS290Chemical stressors of Adverse Outcome Pathways (AOP-Wiki) that are also assayed in ToxCast / Tox21 / ICE.

How many ToxCast-assayed chemicals (CAS) act as molecular initiating-event stressors in at least one AOP-Wiki Adverse Outcome Pathway?
biobricks-ice ↔ biobricks-toxcastCAS9,421ToxCast-screened chemicals (CAS) with Integrated Chemical Environment safety/curation data.

Across the 9,421 shared CAS, which ToxCast-active chemicals carry ICE acute/in-vivo toxicity curation usable for read-across?
biobricks-mesh ↔ biobricks-aopwikiCAS26For the chemical stressors that trigger an Adverse Outcome Pathway, what pharmacological action and disease indexing does MeSH record - i.e. is the AOP-triggering chemical a known drug class?

How many AOP-Wiki chemical stressors are indexed in MeSH, joined on the MeSH registryNumber?
biobricks-mesh ↔ biobricks-iceCAS6,924For a chemical with EPA ICE toxicity/functional-use records, what MeSH indexing does it carry - and via MeSH's pharmacological-action and descriptor mappings, is its tox signal a known pharmacology or an off-target hazard?

How many of EPA ICE's CAS chemicals are indexed in the NLM MeSH vocabulary, joined on the MeSH registryNumber?
biobricks-mesh ↔ biobricks-tox21CAS1,103Which MeSH pharmacological actions are most common among chemicals screened in Tox21, joined on the CAS registry number?

Same crosswalk, coverage angle: how many Tox21 chemicals have a MeSH record on the CAS number, and is that record a descriptor or a supplementary chemical record?
biobricks-mesh ↔ biobricks-toxcastCAS1,146For the chemicals ToxCast screened in its high-throughput assays, which are indexed in MeSH - and what pharmacological action or disease indexing does MeSH attach to the most bioactive ones?

How many ToxCast CAS chemicals carry a MeSH record, joined on the MeSH registryNumber?
biobricks-mesh ↔ sawgraphCAS6For the PFAS and pesticide contaminants SAWGraph measures in environmental samples, which are indexed in MeSH (note: only 6 - MeSH assigns UNII rather than CAS to most of these compounds)?

How many SAWGraph contaminant CAS numbers carry a MeSH registryNumber record?
biobricks-mesh ↔ sockgCAS5For the agricultural chemicals sockg records in soil-carbon field trials, which are indexed in MeSH (note: only 5 - MeSH assigns UNII rather than CAS to most pesticides)?

How many sockg CAS chemicals carry a MeSH registryNumber record?
biobricks-tox21 ↔ biobricks-iceCAS8,916Tox21-screened chemicals (CAS) tied to Integrated Chemical Environment safety/curation data.

How many Tox21 nuclear-receptor and stress-pathway hits (CAS) also have ICE curated in-vivo toxicity records?
biobricks-tox21 ↔ biobricks-toxcastCAS8,909Tox21 high-throughput screening hits (CAS) for chemicals also covered by EPA ToxCast assays.

For chemicals (CAS) screened in both Tox21 and ToxCast, do the assay activity calls agree across the shared set?
biobricks-tox21 → babel → proknCAS→ChEMBL/PubChem3,182Which Tox21-screened chemicals are ChEMBL compounds in ProKN (CAS -> ChEMBL via Babel), and what protein targets does ProKN record for those that are active in Tox21 assays?

How much of the Tox21 chemical library reaches ProKN through Babel, and how many of the bridged chemicals are approved or clinical-stage drugs in ProKN's ChEMBL record?
biobricks-toxcast → babel → proknCAS→ChEMBL/PubChem3,243Which ToxCast chemicals reach ProKN's ChEMBL compounds through Babel (CAS -> ChEMBL), and for an assay target family, do ToxCast activity calls line up with the protein targets ProKN records?

For ToxCast chemicals that are also ProKN compounds, which clinical indications (MeSH, with phase) does ProKN list - i.e. which environmental test chemicals are also drugs?
sawgraph → babel → proknCAS→ChEMBL/PubChem6Which SAWGraph contaminants reach a ProKN compound through Babel, and what does ProKN record about them?

Same crosswalk, coverage angle: which Babel identifier schemes carry SAWGraph's contaminants toward ProKN, and how many arrive?
biobricks-tox21 → babel → rdkgCAS→DrugBank920Which RDKG rare-disease drugs were screened in Tox21 (DrugBank <- CAS via Babel), and in which Tox21 assays are they active?

Of RDKG's DrugBank drugs, how many were Tox21-screened, and which rare diseases do the Tox21-active ones treat?
biobricks-toxcast → babel → rdkgCAS→DrugBank928Which RDKG rare-disease drugs have ToxCast high-throughput assay data (DrugBank <- CAS via Babel), and what do the assays flag?

For a given ToxCast assay endpoint, which active chemicals are RDKG drugs and which rare diseases do they treat?
bio101 → ubergraph → biobricks-aopwikiCHEBI (bio101 label)33Which of the hormones KB Bio 101 teaches (concepts under aura:Hormone) are the biological object of AOP-Wiki key events, what do those key events say happens to the hormone, and which adverse outcomes do the pathways end in?

Rank the KB Bio 101 chemicals that reach AOP-Wiki by the number of key events that act on them and the adverse outcome pathways those key events belong to. How do the textbook's own chemical categories split the ranking?
bio101 → ubergraph → spoke-oknCHEBI (bio101 label)86KB Bio 101 teaches lead, arsenic, mercury, cadmium and DDT. Where does SPOKE-OKN record the matching compounds in the environment: by data source, by medium (air, water, soil), and which counties are the largest air emitters?

Which KB Bio 101 chemicals resolve to SPOKE-OKN compounds, and which of those does SPOKE-OKN link to the most diseases or genes, and what does it mostly record instead?
spoke-okn → ubergraph → biobricks-iceCHEBI↔CAS712Tie an ICE curated-toxicity chemical (CAS) to spoke-okn gene/pathway/disease associations for the same compound via CHEBI.

For SPOKE compounds targeting a specific gene, what ICE curated in-vivo toxicity endpoints are available via the CHEBI->CAS bridge?
spoke-okn → ubergraph → biobricks-tox21CHEBI↔CAS480Tie a Tox21-screened chemical (CAS) to spoke-okn gene/pathway/disease associations for the same compound via CHEBI.

How many of SPOKE's disease-associated compounds have Tox21 high-throughput screening data reachable through the CHEBI->CAS bridge?
spoke-okn → ubergraph → biobricks-toxcastCHEBI↔CAS496Tie a ToxCast chemical (CAS) to spoke-okn gene/pathway/disease associations for the same compound via CHEBI.

Which ToxCast assays cover compounds SPOKE associates with a specific disease such as Parkinson disease, bridged CHEBI->CAS?
biobricks-aopwiki ↔ spoke-oknChEMBL75For an AOP-Wiki chemical stressor with a ChEMBL identity, what bioactivity and drug context does spoke-okn attach to the same compound?

How many AOP-Wiki chemical stressors are present in spoke-okn, joined on the ChEMBL compound id?
biobricks-aopwiki ↔ rdkgDrugBank124Which AOP-Wiki chemical stressors are also drugs in RDKG, joined on the DrugBank id, and how many AOPs and RDKG diseases does each touch?

Same crosswalk, coverage angle: how many of AOP-Wiki's DrugBank ids are RDKG drugs, and how many of those does RDKG link to a disease it treats?
biobricks-aopwiki ↔ spoke-oknDrugBank27Which approved drugs (DrugBank) are chemical stressors of an Adverse Outcome Pathway, and what does spoke-okn record about their targets and indications?

How many AOP-Wiki chemical stressors carry a DrugBank id present in spoke-okn?
rdkg ↔ spoke-oknDrugBank43For drugs SPOKE tracks as chemicals, what disease contraindications or associations does rdkg record?

For an rdkg drug-disease association, which genes and pathways does SPOKE link the same DrugBank drug to?
ruralkg ↔ rdkgDrugBank2Do the substance-use treatment drugs in ruralkg appear in rdkg's drug-disease graph?

Which two DrugBank substance-use treatment drugs from ruralkg appear in rdkg, and what diseases does rdkg attach to them?
rdkg → babel → proknDrugBank→ChEMBL1,816RDKG's rare-disease drugs mapped through Babel (DrugBank -> ChEMBL) to ProKN: which proteins does ProKN say each drug directly physically interacts with?

For an RDKG drug that treats a rare disease, which other indications (MeSH, with clinical phase) does ProKN's ChEMBL record list for the same compound - repurposing context beyond the rare disease?
ruralkg → babel → proknDrugBank→ChEMBL6Which substances in RuralKG's substance-abuse data resolve to ProKN compounds (DrugBank -> ChEMBL via Babel), and what protein targets does ProKN record for them?

For the RuralKG substances that bridge to ProKN, which indications (MeSH, with phase) does ChEMBL list - i.e. which abused substances also have medical uses?
glygenkg ↔ biobricks-pubchem-annotationsGlyTouCan180For the glycans GlyGen attaches at the most human protein sites, what can PubChem's annotations add (mass, and other organisms the glycan is reported in), and which glycan motifs are most widespread across GlyGen's glycoproteins?

How many of glygenkg's glycans does biobricks-pubchem-annotations annotate under their GlyTouCan accession, what share of GlyGen's glycan-bearing sites and proteins do they account for, and what information does PubChem supply for them?
spoke-okn ↔ proknInChIKey143For a chemical spoke-okn tracks (a drug or an environmental toxicant, keyed by InChIKey), what protein targets and ChEMBL bioactivity does prokn record for the same structure?

How many of spoke-okn's chemicals are also in prokn's ChEMBL bioactivity data, joined on InChIKey?
biobricks-mesh ↔ rdkgMeSH474RDKG keys its chemical exposures on MeSH ids. Which MeSH pharmacological actions are most common among them, and to how many RDKG diseases do those exposures contribute?

Same crosswalk, coverage angle: how many of RDKG's chemical exposures resolve to a biobricks-mesh record, of which kind, and how many carry a pharmacological action?
biobricks-aopwiki ↔ biobricks-pubchem-annotationsPubChem CID401For a chemical that triggers an Adverse Outcome Pathway, what curated PubChem toxicology, hazard and pharmacology annotations exist - i.e. which AOPs are triggered by chemicals carrying a given PubChem hazard class?

How many AOP-Wiki chemical stressors carry PubChem annotations, joined on the PubChem CID?
biobricks-aopwiki ↔ spoke-oknPubChem CID87For an AOP-Wiki chemical stressor, what does spoke-okn know about the same compound - its drug/compound identity, protein targets and disease associations?

How many AOP-Wiki chemical stressors are present in spoke-okn, joined on the PubChem CID?
biobricks-pubchem-annotations ↔ spoke-oknPubChem CID762What PubChem free-text annotations (toxicity, hazards, uses) exist for the chemicals SPOKE links to diseases and genes?

For chemicals flagged as carcinogenic or acutely toxic in PubChem free-text annotations, which diseases and genes does SPOKE connect them to (via PubChem CID)?
prokn ↔ biobricks-pubchem-annotationsPubChem CID188,837Which ProKN compounds have the most disease indications, and how many PubChem annotations does biobricks-pubchem-annotations hold for each, joined on the PubChem CID?

Same crosswalk, coverage angle: how many of ProKN's PubChem-keyed compounds have PubChem annotations, overall and among compounds with a disease indication?
biohealth → babel → biobricks-tox21UMLS ↔ chemical id4,307Which conditions does BioHealth's literature most often say are caused by Tox21 chemicals, mapped through Babel to UMLS?

Same crosswalk, coverage angle: how many Tox21 chemicals reach a BioHealth concept through Babel, and of which UMLS semantic type?
biohealth → babel → biobricks-toxcastUMLS ↔ chemical id4,400Which ToxCast chemicals, mapped to BioHealth UMLS concepts through Babel, have the most literature assertions that they cause a condition?

Same crosswalk, coverage angle: how many ToxCast chemicals reach a BioHealth concept through Babel, and of which UMLS semantic type?
biohealth → babel → proknUMLS ↔ chemical id8,488Which BioHealth substances that reach a ProKN compound through Babel have the most literature 'treats' assertions, and how many indications does ProKN record for them?

Same crosswalk, coverage angle: how many of BioHealth's chemical concepts reach ProKN through Babel, and through which ProKN identifier form?
biohealth → babel → rdkgUMLS ↔ chemical id2,387For RDKG drugs mapped to BioHealth through Babel, how does the number of diseases RDKG says each treats compare with the conditions BioHealth's literature says it treats?

Same crosswalk, coverage angle: how many of RDKG's drugs, chemical exposures and chemicals reach a BioHealth concept through Babel?
biohealth → babel → spoke-oknUMLS ↔ chemical id608For SPOKE-OKN compounds with a TREATS edge, mapped to BioHealth through Babel, how do SPOKE's treated diseases compare with BioHealth's literature 'treats' assertions?

Same crosswalk, coverage angle: how many SPOKE-OKN compounds reach a BioHealth concept through Babel, by SPOKE's compound identifier form?
spoke-okn → babel → proknchemical id→ChEMBL/PubChem278Which SPOKE-OKN compounds with a TREATS edge reach a ProKN compound through Babel, and how many ProKN protein targets does each have?

Same crosswalk, coverage angle: how many SPOKE-OKN compounds reach ProKN through Babel, through which ProKN identifier form, and how does that compare with the direct InChIKey join?

Disease & phenotype

KGsShared keyCountExamples
spoke-okn ↔ ndeDOID20Infectious/immune-mediated disease datasets (NDE) for a disease, with that disease's spoke-okn associations, joined on DOID.

For an NDE infectious-disease dataset (DOID), what candidate compounds does spoke-okn associate with that disease, surfacing repurposing leads?
gene-expression-atlas-okn → ubergraph → spoke-oknDOID↔MONDO54spoke-okn gene/compound/prevalence associations for diseases GXA profiles by differential expression, bridged EFO->MONDO->DOID.

Do the genes spoke-okn associates with a disease (DOID) overlap GXA's differentially-expressed genes for the same disease, bridged EFO->MONDO->DOID?
spoke-okn → ubergraph → oard-kgDOID↔MONDO40EHR-derived disease-phenotype associations (OARD, MONDO) for a spoke-okn disease (DOID), bridged through ubergraph.

For an OARD-profiled disease (MONDO), pull spoke-okn's gene and compound associations by bridging MONDO->DOID through ubergraph.
spoke-okn → ubergraph → proknDOID↔MONDO115spoke-okn disease associations (genes/compounds/prevalence/mortality) for diseases ProKN also describes, joined on DOID.

For a ProKN disease with marker-gene proteins, does spoke-okn associate the same genes with the matching DOID disease, bridged MONDO->DOID?
spoke-okn → ubergraph → rdkgDOID↔MONDO149Rare-disease gene/drug associations (rdkg, MONDO) for a spoke-okn disease (DOID), bridged through ubergraph DOID->MONDO.

Do spoke-okn's associated compounds for a disease (DOID) match RDKG's DrugBank treating/contraindicated drugs for the same MONDO disease?
spoke-okn → ubergraph → digcfdekgDOID↔MONDO (+ EFO/Orphanet→MONDO)50spoke-okn disease associations (genes/compounds/prevalence) for diseases CFDE REVEAL has factor inferences on, bridged DOID->MONDO through ubergraph.

For a CFDE REVEAL disease trait (MONDO), which spoke-okn genes for the matching DOID disease overlap the inferred gene-trait factors, bridged MONDO->DOID?
digcfdekg ↔ gene-expression-atlas-oknEFO / Orphanet / MONDO (direct, multi-vocabulary)33Differential-expression studies (GXA) for diseases CFDE REVEAL has gene-trait factor inferences on, matched on EFO/Orphanet/MONDO.

Do the genes GXA finds differentially expressed for a disease overlap the genes CFDE REVEAL ties to the same trait (EFO/Orphanet/MONDO), corroborating inferred factors with expression evidence?
gene-expression-atlas-okn → ubergraph → ndeEFO↔MONDO325NIAID infectious/immune-disease datasets (nde) for diseases GXA profiles by differential expression, via the EFO->MONDO bridge.

How many of NDE's NIAID disease datasets (MONDO) have a corresponding GXA differential-expression study, bridged EFO->MONDO?
gene-expression-atlas-okn → ubergraph → oard-kgEFO↔MONDO159EHR-derived disease-phenotype associations (OARD) for diseases GXA profiles by differential expression, via the EFO->MONDO bridge.

Which OARD diseases with the strongest EHR phenotype signals (MONDO) also have GXA transcriptomic data, via the EFO->MONDO bridge?
gene-expression-atlas-okn → ubergraph → rdkgEFO↔MONDO414Rare-disease gene/drug associations (rdkg) for diseases GXA has differential-expression studies on, via the EFO->MONDO bridge.

Which RDKG rare diseases with known drug treatments (MONDO) also have a GXA differential-expression study, via the EFO->MONDO bridge?
gene-expression-atlas-okn ↔ oard-kgHP13EHR-derived phenotype co-occurrences (OARD) for the phenotypes GXA studies, joined on HP.

For a phenotype GXA profiles by expression (HP), which diseases does OARD show it co-occurring with in EHR data?
gene-expression-atlas-okn ↔ proknHP12ProKN protein/marker-gene evidence for the phenotypes GXA studies, joined on HP.

Do ProKN's marker genes for a phenotype (HP) coincide with the genes GXA finds differentially expressed for the same phenotype?
oard-kg ↔ proknHP4,941Phenotypes clinically associated with rare diseases (OARD) that also have protein/marker-gene evidence (ProKN).

For hepatomegaly (HP), list the marker-gene proteins ProKN attaches alongside the diseases OARD shows it co-occurring with in EHR data.
medical-device-kg → ubergraph → oard-kgHP (MAUDE patient-problem label)314For the most-reported MAUDE patient problems that are HP phenotypes, how many device reports carry each, and how many OARD disease-to-phenotype associations involve that phenotype?

How many MAUDE patient-problem terms map to an HP class by name, how many reach OARD, and which mapped terms does OARD lack?
medical-device-kg → ubergraph → rdkgHP (MAUDE patient-problem label)315For insulin-delivery devices (MAUDE product codes OZP, OZO, QFG, OYC, LZG), which patient problems that are HP phenotypes are reported most, how many RDKG rare diseases present each, and which rare diseases present both of the top two?

How many HP-mapped MAUDE patient-problem terms reach an RDKG rare disease, how many rare diseases does the bridge touch, and which phenotypes connect to the most?
bio101 → ubergraph → oard-kgHP (bio101 label)33Which concepts KB Bio 101 teaches match an HP phenotype term, and how many OARD co-occurrence associations involve each — in which role, how many with a disease, and with how many distinct partner concepts? Rank them, and say which concepts also reach OARD as a MONDO disease through the sibling bridge KB15.

KB Bio 101 teaches Fever as a concept and teaches many infectious and genetic diseases. Which of the textbook's own diseases are associated with fever in OARD's EHR data, with what log-odds ratio and 95% lower bound, in which dataset — and do the textbook's infectious diseases stand out?
bio101 → ubergraph → proknHP (bio101 label)9Which concepts KB Bio 101 teaches match an HP phenotype that ProKN links to genes, and how many genes each? Rank them.

KB Bio 101 teaches polydactyly as a classic inherited trait. Which genes does ProKN associate with the matching HP phenotype, and how many of them belong to MSigDB gene sets for Hedgehog signalling or for cilia — the pathway and organelle developmental biology ties to digit number?
bio101 → ubergraph → rdkgHP (bio101 label)33Which concepts KB Bio 101 teaches match an HP phenotype that RDKG uses, and how many rare diseases present each? Rank them.

When RDKG says a disease KB Bio 101 teaches has a phenotype KB Bio 101 also teaches, which textbook disease → textbook phenotype pairs occur? Do they read like textbook facts?
biomarkerkg ↔ ndeMONDO601Infectious/immune-mediated disease datasets (NDE) for a disease biomarkerkg also tracks, joined directly on MONDO.

Which of the 601 shared MONDO diseases have both an NIAID dataset in NDE and multiple curated biomarkers in BiomarkerKG, prioritizing data-rich infectious diseases?
biomarkerkg ↔ oard-kgMONDO290EHR-derived disease-phenotype associations (OARD) for a biomarkerkg disease, joined directly on MONDO.

How many of BiomarkerKG's MONDO diseases also carry OARD EHR phenotype associations, and which biomarkers map to the most clinically-documented diseases?
biomarkerkg ↔ proknMONDO263Literature biomarkers for a disease (BiomarkerKG) cross-referenced to protein/marker-gene evidence (ProKN).

For colorectal cancer (MONDO), do BiomarkerKG's literature biomarker proteins coincide with ProKN's marker genes for the same MONDO disease, flagging markers that lack molecular evidence?
biomarkerkg ↔ rdkgMONDO754Rare-disease gene/drug associations (rdkg) for a biomarkerkg disease, joined directly on MONDO.

Do BiomarkerKG's biomarker genes for a disease (MONDO) match the disease genes RDKG records for the same MONDO disease, cross-validating markers against rare-disease gene panels?
digcfdekg ↔ ndeMONDO158Which CFDE REVEAL (digcfdekg) disease traits have the most NIAID Data Ecosystem datasets, joined on the MONDO id, and how many genes does digcfdekg associate with each?

Same crosswalk, coverage angle: how many digcfdekg traits are NDE health conditions, by ontology, and how many datasets do they tag?
nde ↔ oard-kgMONDO889NIAID datasets for a disease (NDE) plus its EHR phenotype signature (OARD).

Which MONDO diseases with an NIAID dataset in NDE carry the richest OARD EHR phenotype profiles, ranked by number of associated phenotypes?
nde ↔ proknMONDO756For diseases that ProKN associates with genes, how many NIAID Data Ecosystem datasets study each, joined on the MONDO id?

Same crosswalk, coverage angle: how many diseases do ProKN and NDE share on MONDO, and how many NDE datasets do they tag?
nde ↔ rdkgMONDO2,907Which RDKG diseases have the most datasets in the NIAID Data Ecosystem (NDE), joined on the MONDO id, and which data catalogs hold them?

Same crosswalk, coverage angle: how many of NDE's MONDO health conditions are RDKG diseases, and how many datasets do they tag?
nestkg ↔ biomarkerkgMONDO13For a cancer type whose mutational signal NeST attributes to specific protein systems, which biomarkers does BiomarkerKG list as diagnostic, prognostic or risk markers of that same cancer — and do those biomarkers fall inside the implicated systems?

How many of the 14 NeST cancer types have at least one biomarker in BiomarkerKG?
oard-kg ↔ proknMONDO470Diseases with both EHR phenotype associations (OARD) and marker-gene/protein evidence (ProKN).

How many of OARD's MONDO diseases carry ProKN protein evidence, and which of them accumulate the most marker genes?
prokn ↔ rdkgMONDO2,901Which diseases that RDKG ties to a gene does ProKN record the most indicated compounds for, joined on the MONDO id, and how do RDKG's own gene and treating-drug counts compare?

Same crosswalk, coverage angle: how many diseases do ProKN and RDKG share on the MONDO id, and what does each graph attach to the shared diseases?
rdkg ↔ oard-kgMONDO2,014Rare-disease EHR phenotype profile (OARD) combined with contraindicated/treating drugs (RDKG, DrugBank).

For a DrugBank drug in RDKG, which of the rare diseases it treats also present an EHR phenotype signature in OARD (MONDO)?
biomarkerkg → ubergraph → digcfdekgMONDO (+ EFO/Orphanet→MONDO bridged)193Biomarker-disease associations (biomarkerkg, MONDO) for diseases CFDE REVEAL has gene-trait factor inferences on, joined on MONDO (CFDE's EFO/Orphanet traits bridged to MONDO through ubergraph).

Do BiomarkerKG's biomarker genes for a disease (MONDO) appear among the genes CFDE REVEAL ties to the same trait, cross-checking markers against inferred factors?
digcfdekg → ubergraph → oard-kgMONDO (+ EFO/Orphanet→MONDO bridged)402Rare-disease EHR phenotype profile (OARD) combined with the gene-trait factor inferences CFDE REVEAL records for the same disease.

How many CFDE REVEAL disease traits (MONDO) have a matching OARD EHR phenotype profile that could support their inferred gene-trait factors?
digcfdekg → ubergraph → rdkgMONDO (+ EFO/Orphanet→MONDO bridged)1,045For a rare disease (rdkg, MONDO) with its gene/drug associations, what disease-mechanism factors and gene-trait probabilities does CFDE REVEAL infer?

Do the genes CFDE REVEAL links to a disease trait (MONDO) match RDKG's curated disease genes, validating inferred gene-trait factors against known rare-disease genes?
bio101 → ubergraph → biomarkerkgMONDO (bio101 label)40For the diseases KB Bio 101 teaches, how many BiomarkerKB biomarker assessments name the matching MONDO condition, and of which kind (diagnostic, susceptibility/risk, prognostic, monitoring, predictive)? Rank the bridged diseases, and say where the volume comes from.

For the disorders KB Bio 101 itself classifies as genetic disorders (under aura:Genetic-Disorder), which BiomarkerKB biomarkers are recorded — and, leaving aside the GWAS susceptibility variants, what are the diagnostic, prognostic and monitoring biomarkers, and from which specimen are they measured?
bio101 → ubergraph → digcfdekgMONDO (bio101 label)20Which diseases KB Bio 101 teaches carry PIGEAN gene associations in digcfdekg, how many genes each, how many of them strongly (weight ≥ 5), and under which trait identifier? Rank them.

For the disorders KB Bio 101 itself classifies as genetic disorders (under aura:Genetic-Disorder), which gene does PIGEAN score highest, and how many genes does it score strongly (weight ≥ 5)? For cystic fibrosis, the textbook single-gene example, does CFTR come first?
bio101 → ubergraph → gene-expression-atlas-oknMONDO (bio101 label)27Which diseases KB Bio 101 teaches are studied in Expression Atlas differential-expression experiments, in how many studies and contrasts, and under which disease identifier (MONDO, EFO or Orphanet)? Rank them.

When an Expression Atlas contrast is annotated with a disease KB Bio 101 teaches and is enriched for a process or structure KB Bio 101 teaches, which textbook disease × textbook process pairs occur in the most contrasts? Do they read like textbook pathophysiology?
bio101 → ubergraph → ndeMONDO (bio101 label)60For the diseases KB Bio 101 teaches, how many NDE datasets carry the matching MONDO health condition, and in how many repositories? Rank the bridged diseases.

For the disorders KB Bio 101 itself classifies as genetic disorders (under aura:Genetic-Disorder), which have NDE datasets, how many, and in which repositories? Which textbook genetic disorders have none, and why?
bio101 → ubergraph → oard-kgMONDO (bio101 label)25For the diseases KB Bio 101 teaches, how many OARD co-occurrence associations involve the matching MONDO term, in which role, and with how many distinct partner concepts? Rank the bridged diseases, and say which EHR datasets the evidence comes from.

For two genetic disorders every introductory biology course teaches — KB Bio 101's Sickle-Cell-Anemia and Cystic-Fibrosis — which phenotypes are most strongly associated with them in OARD's EHR data, and does the answer depend on which dataset (structured OMOP records or clinical notes) the evidence comes from? Rank by the lower bound of the 95% confidence interval of the log-odds ratio (robust to small counts), keeping pairs seen in at least 20 patients and a lower bound of at least 3.
bio101 → ubergraph → proknMONDO (bio101 label)32For the diseases KB Bio 101 teaches, how many compounds does ProKN list as indicated for the matching disease, and how many of them are approved (phase 4)? Rank the bridged diseases.

For the disorders KB Bio 101 itself classifies as genetic disorders (under aura:Genetic-Disorder), which approved (phase 4) drugs does ProKN list as indicated? Do they treat the cause or the symptoms?
bio101 → ubergraph → rdkgMONDO (bio101 label)57For the genetic disorders KB Bio 101 teaches (cystic fibrosis, sickle-cell anemia, achondroplasia, ...), which genes does RDKG associate with the matching MONDO disease, and does it recover the textbook causal genes (CFTR, HBB, FGFR3)?

Which of KB Bio 101's textbook diseases carry the most RDKG gene and phenotype associations?
spoke-okn → ubergraph → biomarkerkgMONDO↔DOID107Biomarkers for a disease (BiomarkerKB, MONDO) alongside that disease's spoke-okn gene/compound associations (DOID), bridged DOID<->MONDO through ubergraph.

Do BiomarkerKG's biomarker genes for a disease overlap the genes spoke-okn associates with the same disease, reconciling the two gene sets across the DOID<->MONDO bridge?
oard-kg → ubergraph → proknMONDO↔OMIM11Cross-reference OARD drug/outcome disease associations (oard-kg, MONDO) with ProKN's OMIM-annotated disease evidence by bridging MONDO to OMIM through ubergraph's cross-references.

For a Mendelian disease ProKN annotates by OMIM, what EHR drug-outcome associations does OARD record, bridging OMIM->MONDO through ubergraph?
oard-kg → ubergraph → proknMONDO↔Orphanet316Cross-reference OARD disease associations (oard-kg, MONDO) with ProKN's Orphanet-annotated rare-disease protein evidence by bridging MONDO to Orphanet through ubergraph.

How many of ProKN's Orphanet-annotated rare diseases with protein evidence also surface in OARD's EHR association data, via the MONDO<->Orphanet bridge?
biobricks-mesh → babel → proknMeSH (direct + via babel)3,186Which MeSH disease categories hold the most ProKN disease records, reached directly or through Babel, and how many genes does ProKN associate with them?

Same crosswalk, coverage angle: how many ProKN disease records reach a MeSH record, directly or through Babel?
biobricks-mesh ↔ spoke-oknMeSH_descriptor_id165Map spoke-okn's social-determinants and disease nodes to MeSH (e.g. Social Vulnerability = MeSH D000091482) to pull MeSH definitions / tree placement from biobricks-mesh, or to connect spoke-okn disease nodes to MeSH-tagged concepts - reaching the SDoH layer that the MONDO route (M1) misses.

Starting from a MeSH tree branch (e.g. the Social Determinants of Health descriptor set), enumerate which spoke-okn SDoH and disease nodes fall under it and count the diseases carrying each descriptor.
biobricks-ice ↔ biohealthUMLS46For the biological target of an ICE tox assay (biobricks-ice, a UMLS concept), what clinical / SDoH associations does biohealth attach to that same concept?

How many of ICE's mechanistic-target UMLS concepts does biohealth's literature graph also describe, joined on the UMLS CUI?
biohealth → ubergraph → gene-expression-atlas-oknUMLS↔HP13For a phenotype biohealth tracks (UMLS CUI), is there a GXA differential-expression study on it (HP), bridged through ubergraph UMLS->HP?

Which of GXA's HP-typed differential-expression studies correspond to phenotypes biohealth tracks with SDoH context, via the UMLS->HP bridge?
biohealth → ubergraph → oard-kgUMLS↔HP4,549For a phenotype biohealth tracks (UMLS CUI), what EHR-derived disease co-occurrences does OARD record (HP), bridged through ubergraph UMLS->HP?

Which HP phenotypes with the most OARD EHR disease co-occurrences also carry biohealth SDoH context, via the UMLS->HP bridge?
biohealth → ubergraph → proknUMLS↔HP4,340For a phenotype biohealth tracks (UMLS CUI), what protein / marker-gene evidence does prokn attach (HP), bridged through ubergraph UMLS->HP?

How many of ProKN's HP phenotypes with marker-gene evidence map to a biohealth UMLS concept, and which of those carry SDoH context?
biohealth → babel → digcfdekgUMLS↔MONDO208Which CFDE gene-trait diseases (digcfdekg, MONDO) are also BioHealthKG concepts (MONDO <-> UMLS via Babel), and what does BioHealthKG add about them?

For a digcfdekg disease trait, which genes does the CFDE KG associate with it and which clinical/social concepts does BioHealthKG link to the same disease?
biohealth → babel → nestkgUMLS↔MONDO12Which NeST cancer types (MONDO) are BioHealthKG concepts (MONDO <-> UMLS via Babel), and which NeST protein systems are mutated in them?

For a NeST cancer type, what does BioHealthKG record about the disease alongside NeST's mutated protein systems?
biohealth → ubergraph → biomarkerkgUMLS↔MONDO835For a disease biohealth describes (UMLS CUI), what literature-curated biomarkers does BiomarkerKG record (MONDO), bridged through ubergraph UMLS->MONDO?

Which BiomarkerKG diseases with curated biomarkers (MONDO) also appear in biohealth with SDoH context, bridged MONDO->UMLS?
biohealth → ubergraph → ndeUMLS↔MONDO2,760For a disease biohealth describes (UMLS CUI), what NIAID infectious/immune-disease datasets exist (nde, MONDO), bridged through ubergraph UMLS->MONDO?

For an NIAID dataset disease in NDE (MONDO), what SDoH and clinical associations does biohealth attach, bridged MONDO->UMLS?
biohealth → ubergraph → oard-kgUMLS↔MONDO1,796For a disease biohealth describes (UMLS CUI, with SDoH + clinical context), what real-world EHR phenotype co-occurrences does OARD record (MONDO), bridged through ubergraph UMLS->MONDO?

For type 2 diabetes present in both graphs, contrast biohealth's SDoH determinants against OARD's EHR-derived phenotype co-occurrences for the same MONDO disease.
biohealth → ubergraph → rdkgUMLS↔MONDO9,122For a disease biohealth describes (UMLS CUI, with its SDoH and clinical associations), what rare-disease gene/drug associations does rdkg record (MONDO), bridged through ubergraph UMLS->MONDO?

For a rare disease RDKG has drug associations for (MONDO), what SDoH and clinical associations does biohealth attach via its UMLS CUI, bridged MONDO->UMLS?
biohealth → ubergraph → spoke-oknUMLS↔MONDO↔DOID173For a disease biohealth describes (UMLS CUI), pull its spoke-okn gene / compound / prevalence associations (DOID), bridged through ubergraph UMLS->MONDO->DOID.

For a spoke-okn disease with prevalence/mortality data (DOID), what social-determinant associations does biohealth carry, bridged DOID->MONDO->UMLS?
biobricks-mesh → babel → ndedisease id→MeSH3,467Through Babel, how do the NIAID Data Ecosystem's datasets distribute over MeSH disease categories, by their health-condition terms?

Same crosswalk, coverage angle: how many of NDE's health-condition terms reach a MeSH record through Babel, by the ontology of the NDE term?
biobricks-mesh → babel → rdkgdisease id→MeSH7,934Through Babel, which MeSH disease categories hold the most RDKG diseases?

Same crosswalk, coverage angle: how many RDKG diseases reach a MeSH record through Babel, and is it a main descriptor or a supplementary disease record?
biohealth → babel → prokndisease id→UMLS2,958Which BioHealth disease concepts reached from ProKN's disease records through Babel have the most 'treats' assertions in BioHealth's literature-derived statements?

Same crosswalk, coverage angle: how many ProKN disease records reach a BioHealth UMLS concept through Babel, and how many BioHealth concepts do they land on?

Earth observation

KGsShared keyCountExamples
climatemodelskg ↔ nasa-gesdisc-kgGCMD instrument342For an Earth-observation instrument a climate-modeling paper in climatemodelskg mentions (e.g. MODIS), what NASA GES DISC datasets and platforms does nasa-gesdisc-kg catalogue for that same instrument?

How many of the instruments named in climatemodelskg's climate-modeling literature are also GCMD-catalogued instruments in nasa-gesdisc-kg, joined on the instrument name?
climatemodelskg ↔ nasa-gesdisc-kgGCMD platform236For a satellite platform a climate-modeling paper in climatemodelskg mentions (e.g. Aqua), which instruments and NASA GES DISC datasets does nasa-gesdisc-kg catalogue for that same platform?

How many of the platforms named in climatemodelskg's climate-modeling literature are also GCMD-catalogued platforms in nasa-gesdisc-kg, joined on the platform name?

Environmental toxicology

KGsShared keyCountExamples
biobricks-aopwiki ↔ sockgCAS8Which SOCKG agrochemicals are AOP-Wiki chemicals, and which Adverse Outcome Pathways name them as stressors?

Same crosswalk, coverage angle: how many of SOCKG's agrochemicals does AOP-Wiki carry?
biobricks-tox21 ↔ sockgCAS55Which pesticide active ingredients used in SOCKG's soil-carbon field experiments were screened in Tox21, and how often are they applied?

Same crosswalk, coverage angle: how many of SOCKG's agrochemicals are in Tox21, compared with ToxCast and ICE?
sawgraph ↔ biobricks-iceCAS44For the contaminants measured in SAWGraph, what does ICE record - the standardized chemical identity (name, DTXSID) and functional-use categorization of the environmental contaminants?

Across the 39 CAS contaminants shared with SAWGraph, which ICE curated-data-domain records (e.g. acute toxicity, endocrine activity) are populated, and which contaminant carries the most curated toxicity endpoints?
sawgraph ↔ biobricks-tox21CAS11Which contaminants measured in SAWGraph were screened in Tox21, and how many SAWGraph observations does each have?

Same crosswalk, coverage angle: how many SAWGraph contaminants are in Tox21, compared with ToxCast?
sawgraph ↔ biobricks-toxcastCAS34For the contaminants measured in SAWGraph's environmental water samples, how many ToxCast high-throughput assay endpoints exist, and what is each chemical's environmental footprint?

Ranked by ToxCast assay-endpoint hit count, which CAS contaminants detected in SAWGraph water samples show the broadest high-throughput bioactivity, and at which sampling locations do they occur?
sockg ↔ biobricks-iceCAS68For a pesticide sockg records applied to a field soil (by CAS), what curated toxicity / hazard data does biobricks-ICE hold for that same chemical?

How many of the agrochemicals sockg tracks in soil have ICE toxicological screening data, joined on CAS?
sockg ↔ biobricks-toxcastCAS59For a soil-applied pesticide sockg tracks (by CAS), what ToxCast high-throughput assay activity is recorded for the same chemical?

Which of sockg's soil agrochemicals appear in EPA ToxCast, joined on CAS?

Function & Pathways

KGsShared keyCountExamples
pankgraph ↔ proknGO16,970Which pancreatic-islet genes (pankgraph) and ProKN proteins are annotated with the same GO function, e.g. insulin secretion or glucose homeostasis?

Which GO terms are shared by the most pankgraph islet genes and ProKN proteins, and how many protein–gene pairs does each such term bridge across the two graphs?
bio101 → ubergraph → biobricks-aopwikiGO (bio101 label)47Which KB Bio 101 processes are the biological process of AOP-Wiki key events, and which textbook cell structures are the object a key event acts on? Rank the bridged concepts by key events and adverse outcome pathways.

For the structures KB Bio 101 itself classifies as organelles (under aura:Organelle), which AOP-Wiki key events act on them as their biological object, what do those key events say happens, and which adverse outcomes do their pathways end in?
bio101 → ubergraph → gene-expression-atlas-oknGO (bio101 label)193Which processes and cell structures KB Bio 101 teaches come up as GO terms enriched in Expression Atlas differential-expression contrasts, and in how many contrasts and experiments? Rank the top 40.

For the plant processes and structures KB Bio 101 teaches (photosynthesis, photorespiration, carbon fixation, gravitropism, phototropism, photomorphogenesis, flower development, systemic acquired resistance, the photosystems, chloroplast, thylakoid), in how many Expression Atlas contrasts and experiments are they enriched, and which experimental comparisons enrich photosynthesis most strongly?
bio101 → ubergraph → pankgraphGO (bio101 label)200Which KB Bio 101 textbook processes match GO biological-process terms that pankgraph's genes are annotated with, and, for exocytosis (the mechanism by which a beta cell releases insulin), which genes does pankgraph place on that term, how many of them are islet (beta-cell) genes, and what does the textbook say the process is?

Of the KB Bio 101 textbook concepts that reach pankgraph through GO, which carry the largest gene sets, and which carry the largest islet gene sets, counting only genes with a PanKbase beta-cell expression record? How much of pankgraph's GO-annotated gene catalogue does the textbook vocabulary reach at all?
bio101 → ubergraph → proknGO (bio101 label)309KB Bio 101 teaches cellular respiration as a sequence of stages (glycolysis, pyruvate oxidation, the citric acid cycle, oxidative phosphorylation). For each stage, which human proteins does ProKN annotate to the matching GO process, set beside what the textbook says that stage consumes and produces? Which stages does the exact-name bridge fail to reach?

Among the structures KB Bio 101 itself files as cell structures (mitochondrion, ribosome, lysosome and so on), which carry the most human ProKN protein annotations through their matching GO cellular-component term? Which familiar structures does the exact-name bridge, or the textbook's own classification, leave out?
gene-expression-atlas-okn ↔ proknReactome1,068For a disease GXA finds a Reactome pathway differentially active in, which proteins (ProKN) make up that pathway?

For a Reactome pathway whose member proteins are catalogued in ProKN (via biolink:participates_in), in which GXA disease contrasts is that pathway reported differentially active, and in what direction?

Genes

KGsShared keyCountExamples
biobricks-aopwiki ↔ gene-expression-atlas-oknEnsembl1,355Baseline tissue expression (GXA) for genes implicated as AOP key-event targets (AOP-Wiki).

Which AOP-Wiki key events target genes whose GXA baseline expression is restricted to a single tissue such as liver or kidney?
biobricks-aopwiki ↔ spoke-oknEnsembl1,385Gene targets of AOP molecular initiating / key events (AOP-Wiki) with their spoke-okn network/disease/compound associations.

For an AOP-Wiki molecular initiating event triggered by a given stressor, which spoke-okn diseases and compounds are linked to its target genes?
gene-expression-atlas-okn ↔ spoke-oknEnsembl15,132One-query gene dossier: baseline tissue expression (GXA) for any spoke-okn gene, plus its network/disease/compound associations — and pankgraph's islet context on the same Ensembl id, free.

Among spoke-okn genes associated with a given disease, which show the highest GXA baseline expression in the disease-relevant tissue?
glygenkg ↔ gene-expression-atlas-oknEnsembl7,950For the genes whose proteins carry the most distinct glycan structures in GlyGen (LAMP1, PIGR, CLU, FN1), in how many Expression Atlas contrasts is each gene differentially expressed, and in which direction?

How many of glygenkg's 7,959 Ensembl gene loci are Expression Atlas genes, and how many have a differential-expression result?
glygenkg ↔ pankgraphEnsembl7,953Which of PanKgraph's type 1 diabetes genes encode a protein that is glycosylated in GlyGen (PIGR, CD63, HLA-DRB1, IL2RA), and how many glycosylated residues and glycans does each carry?

How many of glygenkg's 7,959 Ensembl gene loci are PanKgraph genes, and how many of those are expressed in beta cells?
glygenkg ↔ spoke-oknEnsembl7,315For the genes whose proteins carry the most N-glycosylated residues in GlyGen (LRP1, SORL1, PTPRC, APOB), which diseases does SPOKE associate with each gene?

How many of glygenkg's 7,959 Ensembl gene loci are SPOKE genes, and how many of those have a SPOKE disease association?
pankgraph ↔ gene-expression-atlas-oknEnsembl60,581For a pancreatic-islet gene (pankgraph), which GXA differential-expression contrasts is it significant in?

Among pankgraph's beta-cell-expressed genes (biolink:expressed_in CL_0000169), which are differentially expressed in GXA's diabetes contrasts?
pankgraph ↔ proknEnsembl37,835For canonical pancreatic-islet genes pankgraph catalogues (INS, PDX1, MAFA, NKX6-1, GCG), what MSigDB pathways / encoded protein does ProKN annotate, joined on the Ensembl gene id?

Which MSigDB pathway in ProKN is shared by the most pankgraph-catalogued islet genes, joined on the Ensembl gene id?
pankgraph ↔ spoke-oknEnsembl16,314For any spoke-okn gene, add pankgraph's islet context (islet cell-type expression, gene network, GO function) on the shared Ensembl id.

Of the 176 genes pankgraph associates with type 1 diabetes (MONDO_0005147), which does spoke-okn know, and what compounds target them?
prokn ↔ spoke-oknEnsembl16,140How many genes do prokn and spoke-okn share on the Ensembl id, joined DIRECTLY with no bridge graph?

For a spoke-okn disease-associated gene, pull prokn's reified source-attributed evidence, its marker-gene role (HAS_MARKER_GENE) and its tissue expression on the shared Ensembl id — without routing through wikidata.
biobricks-aopwiki ↔ rdkgEntrez1,193AOP key-event target genes (AOP-Wiki) that are also rare-disease genes (rdkg) - toxicology pathway meets rare-disease genetics.

For a given rare disease in rdkg, which AOP-Wiki molecular initiating or key events involve its causative Entrez genes?
biobricks-aopwiki ↔ spoke-genelabEntrez1,472Gene targets of AOP molecular initiating / key events (AOP-Wiki) that have spaceflight/omics evidence in spoke-genelab.

Which AOP-Wiki adverse outcome pathways are over-represented among genes differentially expressed under spaceflight in spoke-genelab?
biobricks-ice ↔ rdkgEntrez358For a gene targeted by an ICE tox assay (biobricks-ice, Entrez), what rare-disease associations does rdkg record for that same gene?

How many of the mechanistic gene targets of ICE toxicology assays are rare-disease genes in rdkg, joined on Entrez?
biomarkerkg ↔ digcfdekgEntrez200Which clinical biomarker genes also carry a CFDE gene-trait association, and do the two agree on the disease?

How many BiomarkerKG gene analytes appear in digcfdekg?
biomarkerkg ↔ rdkgEntrez167Which rare-disease genes in RDKG are also used as clinical biomarkers, and for which (usually different) common diseases?

How many BiomarkerKG gene analytes appear in RDKG?
biomarkerkg ↔ spoke-genelabEntrez200Are the genes used as clinical biomarkers on Earth differentially expressed in spaceflight, per the GeneLab contrasts?

How many BiomarkerKG gene analytes appear in spoke-genelab?
biomarkerkg ↔ spoke-oknEntrez191For a gene whose expression level BiomarkerKG treats as a biomarker, what does SPOKE add — the disease associations, compounds and pathways of that same gene?

How many BiomarkerKG gene analytes have a SPOKE gene node?
digcfdekg ↔ rdkgEntrez8,934Rare-disease genes (rdkg) with the disease-mechanism factors and trait associations CFDE REVEAL infers for them.

Which CFDE REVEAL-inferred traits recur across the most rdkg rare-disease genes, and for which rare diseases?
digcfdekg ↔ spoke-genelabEntrez19,747CFDE REVEAL gene/trait/factor inferences for genes that also have spaceflight/omics observations in spoke-genelab (NASA GeneLab).

How many genes carry both a CFDE REVEAL trait/factor inference and a spaceflight expression change in spoke-genelab?
digcfdekg ↔ spoke-oknEntrez16,052CFDE REVEAL gene/trait/factor inferences enriched with that gene's network/disease/compound associations in spoke-okn.

For a spoke-okn drug's target genes, what trait and disease-mechanism factor inferences does CFDE REVEAL provide?
rdkg ↔ gene-expression-atlas-oknEntrez9,219Which RDKG genes with a variant on record as causing a rare disease are strongly differentially expressed in human Expression Atlas contrasts?

How many RDKG genes are also Expression Atlas gene nodes, and how many of RDKG's causal-variant genes have expression records there?
rdkg ↔ spoke-genelabEntrez9,034Rare-disease genes (rdkg) with their spaceflight/omics observations in spoke-genelab (NASA GeneLab).

How many spoke-genelab spaceflight differentially expressed genes are known rare-disease genes in rdkg?
rdkg ↔ spoke-oknEntrez8,475Rare-disease gene associations (rdkg: gene_associated_with_condition / has_gene) enriched with that gene's network/disease/compound associations in spoke-okn.

For the causative genes of a specific rare disease in rdkg, which spoke-okn compounds and pathways are associated?
spoke-genelab ↔ spoke-oknEntrez16,326GeneLab spaceflight/omics gene observations (spoke-genelab) joined to that gene's network/disease/compound associations in spoke-okn, directly on the shared Entrez gene id.

For a spoke-okn disease of interest, which of its associated genes show spaceflight expression changes in spoke-genelab on the shared Entrez id?

Also worked: example 1 · example 2
biobricks-ice → babel → glygenkgEntrez→Ensembl187Which of ICE's assay target genes encode proteins that GlyGen records as glycosylated, ranked by the number of distinct glycans, and which assay providers test them?

How many of ICE's assay target genes reach a glygenkg gene through Babel, how many have a mapped glycosylation site, and how does coverage differ by assay provider?
biobricks-ice → babel → pankgraphEntrez→Ensembl395Which ICE (Integrated Chemical Environment) assays target genes that PanKGraph annotates in the pancreas (Entrez -> Ensembl via Babel)?

How many of ICE's assay target genes reach PanKGraph through Babel, and which pancreas-relevant genes are the most-assayed targets?
biomarkerkg → babel → pankgraphEntrez→Ensembl200Which BiomarkerKG gene biomarkers are PanKGraph pancreas genes (Entrez <-> Ensembl via Babel), and for which diseases are they biomarkers?

Of BiomarkerKG's 201 gene biomarkers, how many reach PanKGraph through Babel, and which are associated with diabetes or pancreatic disease?
digcfdekg → babel → glygenkgEntrez→Ensembl7,928For the genes whose proteins carry the most distinct glycan structures in GlyGen (PSAP, TF, KNG1, LAMP2), which traits does the CFDE gene-trait graph link them to most strongly?

How many of glygenkg's gene loci bridge to a digcfdekg gene through Babel, and how many carry a gene-to-trait association?
digcfdekg → babel → pankgraphEntrez→Ensembl34,013Which CFDE gene-trait associations (digcfdekg) involve PanKGraph pancreas genes (Entrez <-> Ensembl via Babel), e.g. for diabetes-related traits?

For a PanKGraph type 1 diabetes gene, which traits and factors does the CFDE KG attach to it?
digcfdekg → wikidata → proknEntrez→Ensembl7,965For genes CFDE REVEAL implicates in a trait, what GO functions, pathways and reified protein evidence does ProKN annotate on the shared gene (Entrez->Ensembl via Wikidata)?

Starting from a ProKN gene's GO / pathway annotation, which CFDE REVEAL traits is that gene associated with, joined on the Ensembl id bridged from Entrez through Wikidata?
rdkg → babel → glygenkgEntrez→Ensembl4,327Which genes behind RDKG's congenital disorders of glycosylation encode a protein that GlyGen itself records as glycosylated, and at how many residues?

How many of glygenkg's gene loci bridge to an RDKG rare-disease gene through Babel, and which rare diseases have the most genes encoding GlyGen glycoproteins?
rdkg → babel → pankgraphEntrez→Ensembl9,159Which RDKG rare-disease genes are expressed or annotated in PanKGraph's pancreas data (Entrez <-> Ensembl via Babel), e.g. for monogenic diabetes?

How many of RDKG's disease genes reach PanKGraph's Ensembl genes through Babel, and which rare diseases do the pancreas-relevant ones cause?
spoke-genelab → babel → glygenkgEntrez→Ensembl7,932Which mouse orthologs of GlyGen's glycan-richest genes (haptoglobin, transferrin, kininogen) are differentially expressed in liver in clean spaceflight-versus-ground-control contrasts, and in which direction?

How many of glygenkg's gene loci bridge to a GeneLab gene through Babel, and how many have a mouse ortholog GeneLab has measured?
spoke-genelab → babel → pankgraphEntrez→Ensembl28,554Which genes differentially expressed in spaceflight (SPOKE-GeneLab) are PanKGraph pancreas / type 1 diabetes genes (Entrez <-> Ensembl via Babel)?

How large is the gene overlap between SPOKE-GeneLab and PanKGraph through Babel, and which PanKGraph gene annotations do spaceflight-responsive genes carry?
digcfdekg → wikidata → proknEntrez→HGNC20,783For genes ProKN tracks as protein marker genes (HGNC), what disease-mechanism factors and trait associations does CFDE REVEAL infer?

For a given CFDE REVEAL trait or disease-mechanism factor, which of the implicated genes does ProKN annotate as protein marker genes (HGNC, via Wikidata)?
prokn → wikidata → spoke-oknHGNC→Entrez16,298Protein marker genes for a cell type / tissue (ProKN HAS_MARKER_GENE, HGNC) mapped via Wikidata to their spoke-okn network/disease/compound associations.

For a spoke-okn disease-associated gene, which cell type or tissue does ProKN flag it as a protein marker of (HGNC, via Wikidata)?

Geospatial

KGsShared keyCountExamples
climatemodelskg ↔ spoke-oknGeoNames106For a location climatemodelskg holds climate-model output for (by GeoNames id), what biomedical / environmental / SDoH data does spoke-okn attach to that same place?

How many of climatemodelskg's GeoNames-identified locations are also geographic entities in spoke-okn, joined on the GeoNames place id?
sockg ↔ spatialkgKWG_county62Aggregate SOCKG soil-carbon / GHG-flux measurements to the county (FIPS) level and join them to spatialkg's admin-region hierarchy for state-level summaries.

Which states hold the most SOCKG soil-carbon experiment counties when the 62 counties are rolled up through the spatialkg admin hierarchy?
wildlifekn ↔ spatialkgKWG_county2,575For wildlifekn's county reference nodes in one state (e.g. Indiana), which spatialkg county does each resolve to through its KnowWhereGraph IRI, and how many S2 Level-13 cells does the hub place in it?

How many of the KnowWhereGraph IRIs wildlifekn carries are nodes in spatialkg, and which are not?
fiokg ↔ sawgraphS2_L132,166In Maine, find S2 cells where a sawgraph PFAS sample co-occurs with an EPA FRS facility (fiokg) - especially EPA-PFAS-Facility-typed ones - to relate PFAS detections to nearby potentially-PFAS-handling facilities.

Across Maine, how many EPA FRS facilities (fiokg) share an S2 Level-13 cell with at least one sawgraph PFAS detection, and which FRS facility types dominate those co-located cells?
fiokg ↔ spatialkgS2_L13681,045Place EPA FRS facilities (fiokg) on the national S2 grid (spatialkg), roll them up to county/state admin regions, and find which facilities share an S2 cell with PFAS samples (sawgraph) or hydrologic features (hydrologykg).

Which S2 Level-13 cells hold the most EPA FRS facilities (fiokg) nationally, and which county/state do those facility-dense cells roll up to on the spatialkg admin hierarchy?
hydrologykg ↔ spatialkgS2_L13106,138Place Illinois wells/streams (hydrologykg) on the national S2 grid and roll up to county via spatialkg admin regions.

After rolling hydrologykg S2 cells up through the spatialkg admin regions, how many wells vs streams fall in each Illinois county?
medical-device-kg ↔ spatialkgS2_L1316,977In which Minnesota counties do the state's FDA-registered medical-device establishments sit, placed on computed S2 Level-13 cells and rolled up through spatialkg - and what happens to an establishment whose cell crosses a county line?

How many geocoded medical-device-kg sites (establishments and mammography facilities) resolve to a spatialkg S2 Level-13 cell, and which fall outside the grid?
sawgraph ↔ spatialkgS2_L134,814Aggregate Maine PFAS samples (sawgraph) to S2 cells and counties (spatialkg).

Which Maine counties contain the most S2 cells with sawgraph PFAS samples once rolled up through the spatialkg admin hierarchy?
sockg ↔ sawgraphS2_L132Which USDA soil-organic-carbon (SOCKG) experiment sites sit in the same S2 Level-13 cell as a SAWGraph water-quality sample, and what PFAS analytes were screened there?

Which SAWGraph water-quality samples fall in the same S2 Level-13 cell as a USDA SOCKG soil-organic-carbon site, and what soil-carbon treatments run at that site?
sockg ↔ spatialkgS2_L131,069Place SOCKG soil-organic-carbon experiment sites on the national S2 grid (spatialkg) and roll them up to county/state admin regions.

How many distinct counties host SOCKG soil-organic-carbon experiment sites once their S2 cells are rolled up through the spatialkg admin regions?
sudokn ↔ spatialkgS2_L1342,560Place SUDOKN manufacturers of a NAICS on the S2 grid (computed) and find which cells also contain a sawgraph PFAS sample or an EPA facility (fiokg), with the county each sits in. E.g. SUDOKN electroplaters (332813) sharing a cell with a PFAS sample.

Aggregate computed-S2 SUDOKN manufacturer locations up to the county via spatialkg admin regions to rank counties by manufacturer density for a given NAICS.
ufokn ↔ fiokgS2_L1319,252Which urban flood-risk cells (ufokn) contain EPA-regulated facilities (fiokg)? - flood exposure of regulated sites, co-located in the same S2 Level-13 cell.

How many EPA-regulated facilities (fiokg) sit inside a ufokn flood-risk S2 cell, and which facility types are the most flood-exposed?
ufokn ↔ spatialkgS2_L1397,087Place urban-flooding Risk-Points and built-environment features (ufokn) on the national S2 Level-13 grid (spatialkg), roll them up to county/state admin regions, and find which flood risk cells also contain EPA FRS facilities (fiokg), PFAS samples (sawgraph) or hydrologic features (hydrologykg).

Which counties accumulate the most ufokn flood Risk-Points once their S2 Level-13 cells are rolled up through the spatialkg admin regions?
dreamkg ↔ ruralkgZIP5127In Los Angeles and Philadelphia ZIPs, where do dreamkg's social services (shelter, food, medical care) co-locate with ruralkg's substance-use treatment facilities - i.e. which neighborhoods have treatment access but a social-service desert, or vice versa?

How many ZIPs are shared between dreamkg's social-service locations and ruralkg's treatment facilities?
dreamkg ↔ scalesZIP5235Which federal district court has jurisdiction over the ZIPs where Los Angeles and Philadelphia social services (shelter, food, medical care) are located?

How many dreamkg social-service ZIPs fall within a scales federal-district-court jurisdiction territory?
medical-device-kg ↔ dreamkgZIP5232In the neighbourhoods DreamKG serves, which FDA-registered device establishments and mammography facilities are present — a device-access read on a social-service catchment?

How many DreamKG social-service ZIPs also carry a medical-device-kg address?
medical-device-kg ↔ ruralkgZIP55,141Do the ZIPs of rural-health and opioid-treatment facilities also host FDA-registered device establishments, or are device manufacturing and servicing concentrated elsewhere?

How many ruralkg facility ZIPs also appear in medical-device-kg?
medical-device-kg ↔ scalesZIP518,654Which federal district court has jurisdiction over the ZIP of a device firm named in an FDA recall, and what litigation does SCALES record there?

How many medical-device-kg ZIPs fall inside a SCALES federal-district-court jurisdiction territory?
medical-device-kg ↔ spoke-oknZIP519,095Which counties and health outcomes does SPOKE record for the ZIPs where FDA-registered device establishments, X-ray assembler sites and mammography facilities sit?

How many distinct US ZIP codes in medical-device-kg resolve to a SPOKE location node?
medical-device-kg ↔ sudoknZIP510,697In the ZIPs where SUDOKN records manufacturing capability, which FDA-registered medical-device establishments and recalls are on file — i.e. where does the supply-chain graph meet the device-regulation graph?

How many SUDOKN manufacturer ZIPs also carry a medical-device-kg establishment, assembler site or recall address?
ruralkg ↔ scalesZIP55,297Which federal district court has jurisdiction over the ZIP where a given opioid-treatment or rural-health facility is located, and what case activity does scales record there?

How many ruralkg facility ZIPs fall within a scales federal-district-court jurisdiction territory?
securechainkg ↔ spoke-oknZIP54,375In the ZIP codes where securechainkg locates the most manufacturers, how many environmental chemicals does spoke-okn report found?

How many securechainkg manufacturer-site ZIP codes are ZIP nodes in spoke-okn, and what shapes do the raw ZIP values take?
spoke-okn ↔ dreamkgZIP5235For Los Angeles or Philadelphia ZIPs, list DREAM-KG homelessness/social services in a ZIP alongside spoke-okn's local context.

How many DREAM-KG social services are located in each Los Angeles or Philadelphia ZIP, and which ZIPs carry spoke-okn environmental burden yet list no services?
spoke-okn ↔ ruralkgZIP55,390Combine spoke-okn ZIP-level context with ruralkg rural health/justice indicators for the same ZIP, and roll up to county via ruralkg's KWG censusCounty.

For a rural ZIP flagged by ruralkg's health indicators, what spoke-okn environmental context applies at the same ZIP5?
spoke-okn ↔ sudoknZIP513,647For a ZIP where SUDOKN lists small/medium manufacturers, what does spoke-okn record about that place - its county, air quality, and health/care context?

How many ZIP codes are shared between sudokn's manufacturer addresses and spoke-okn's ZIP geography?
medical-device-kg ↔ climatemodelskgcountry code (FIPS 10-4 / ISO 3166-1 alpha-2)145Which countries manufacture the devices behind the most MAUDE adverse-event reports, and how much flood, drought, heat, fire and storm literature does climatemodelskg link to each of the top ten outside the US?

Which code system do MAUDE's country fields use - FIPS 10-4 or ISO 3166-1 - and which codes name a different country in each, so that an ISO join silently relocates reports?
climatemodelskg → spoke-okn → spatialkgcounty_FIPS947For a US county with PFAS contamination or environmental burden on the SAWGraph spatial hub, which climate-modeling publications reference places in that same county?

How many US counties on the SAWGraph spatial hub contain a location referenced by climatemodelskg, joined on the assembled county FIPS?
fiokg ↔ spatialkgcounty_FIPS3,031Aggregate EPA FRS facilities (fiokg) to the county, place those counties on the spatialkg admin-region hierarchy, and join to county-keyed members (e.g. SCALES federal-court activity, ruralkg rural-resilience indicators) for the same county.

For a given county, count its EPA FRS facilities (fiokg) and use the spatialkg admin hierarchy to find neighboring counties carrying a comparable facility burden.
fiokg ↔ spoke-okncounty_FIPS3,032For a county, combine EPA FRS facility counts/types (fiokg) with spoke-okn's county-level environmental and health indicators, and roll up to state via the shared FIPS.

Rank counties where high EPA FRS facility density (fiokg) coincides with poor spoke-okn county health indicators at the same FIPS.
geoconnex ↔ spatialkgcounty_FIPS3,114Roll geoconnex hydrologic monitoring features up to the county, then place those counties on the spatialkg S2 grid / admin-region hierarchy to pull neighboring counties or state-level rollups.

How many geoconnex hydrologic monitoring features does each county hold, and which counties on the spatialkg admin hierarchy have none (monitoring gaps)?
geoconnex ↔ spoke-okncounty_FIPS3,184For a county, combine geoconnex's water-monitoring features with spoke-okn's local environmental/health context, and roll up to state via the shared FIPS.

For counties lacking geoconnex water-monitoring features, what spoke-okn environmental/health burden is reported at the same FIPS, flagging under-monitored at-risk counties?
nikg ↔ spatialkgcounty_FIPS2Place nikg Philadelphia/Chicago neighborhood-incident data on the spatialkg admin-region hierarchy and compare the two counties' state-level context.

Which states (Illinois vs Pennsylvania) do nikg's two neighborhood-incident counties roll up to on spatialkg, and how do their state-level admin contexts differ?
nikg ↔ spoke-okncounty_FIPS2Join nikg Philadelphia neighborhood-incident counts with spoke-okn's Philadelphia-County environmental/health indicators.

For Cook County (Chicago), pair nikg neighborhood-incident counts with spoke-okn's Cook-County environmental/health indicators at the same FIPS.
scales ↔ spatialkgcounty_FIPS3,029Aggregate SCALES federal court cases to the county of filing and place those counties on the spatialkg S2 grid / admin-region hierarchy for state-level or neighboring-county justice summaries.

Which counties file the most SCALES federal court cases, and which neighboring counties on the spatialkg admin hierarchy fall in the same district?
scales ↔ spoke-okncounty_FIPS3,096For a county, combine SCALES federal court case volume/charges with spoke-okn's county-level environmental and health indicators.

In counties with elevated spoke-okn pollution indicators, how many SCALES federal cases carry environmental charges at the same county FIPS?
spoke-okn ↔ ruralkgcounty_FIPS3,196Join spoke-okn county-level environmental/health rollups with ruralkg rural-resilience (health + justice) indicators for the same county FIPS.

Which counties show both weak ruralkg rural-resilience justice indicators and elevated spoke-okn environmental burden at the same county FIPS?
spoke-okn ↔ sockgcounty_FIPS31For counties with SOCKG soil-carbon experiment sites, pull spoke-okn's county-level environmental/health context.

How many of the 31 SOCKG soil-carbon counties also register elevated spoke-okn environmental indicators at the matching FIPS?
spoke-okn ↔ spatialkgcounty_FIPS3,122Aggregate spoke-okn ZIP-level environmental/health data to the county, then place those counties on the spatialkg S2 grid / admin-region hierarchy and pull neighboring counties or state rollups.

For a given county, which neighboring counties on the spatialkg admin hierarchy carry a similar spoke-okn environmental/health profile?
wildlifekn ↔ spatialkgcounty_FIPS63Roll wildlifekn bird/amphibian observations up to the Florida county and join county-level PFAS (sawgraph), EPA facilities (fiokg) or health (spoke-okn) via spatialkg county FIPS.

How many Florida counties carry wildlifekn amphibian/bird observations, and which of those also register sawgraph PFAS detections in the same county FIPS?
wildlifekn ↔ spoke-okncounty_FIPS2,810For wildlifekn's county reference nodes in one state (e.g. Indiana), what rural share and life expectancy does spoke-okn report for each county?

How many wildlifekn county FIPS codes resolve to a spoke-okn county node, and which do not?
geoconnex ↔ spatialkgstate_FIPS51Roll geoconnex hydrologic features up to the state and join state-level summaries to the spatialkg admin-region hierarchy.

Which states have the densest geoconnex hydrologic-feature coverage per the spatialkg AdministrativeRegion_1 state regions?
spoke-okn ↔ sockgstate_FIPS18Compare spoke-okn state-level environmental/health summaries with the states where SOCKG runs soil-carbon experiments.

Which of the 18 states running SOCKG soil-carbon experiments rank highest on spoke-okn's state-level environmental summaries?
spoke-okn ↔ spatialkgstate_FIPS51Roll spoke-okn data up to the state and join state-level summaries to the spatialkg admin-region hierarchy.

Which states, aligned to the 51 spatialkg AdministrativeRegion_1 regions, show the widest spoke-okn county-to-county spread in environmental/health indicators?
sudokn ↔ spatialkgstate_FIPS51Roll SUDOKN manufacturers up to the state and join state-level summaries (counts by NAICS, capability, certificate) to the spatialkg admin hierarchy or any state_FIPS-keyed member (spoke-okn, geoconnex, sockg). E.g. SUDOKN electroplaters (NAICS 332813) per state vs EPA-regulated facilities.

Which states host the largest SUDOKN aerospace/metal-parts manufacturing base by NAICS when aligned to the spatialkg state admin regions?

Hydrology

KGsShared keyCountExamples
geoconnex ↔ hydrologykgCOMID11,392For a named river mainstem in geoconnex, what NHDPlus flowline attributes (reach code, feature type, flow-path length) and public-water-system context does hydrologykg record for the same reach?

How many NHDPlus reaches are shared between geoconnex and hydrologykg, joined on the NHDPlus COMID?

Industry & supply chain

KGsShared keyCountExamples
fiokg ↔ securechainkgNAICS301Cross-reference the NAICS industries of SecureChain supply-chain participants and SUDOKN manufacturers with the EPA FRS facilities (fiokg) in those same industries, then locate those facilities on the spatial hub via fiokg's S2/county links.

For each NAICS code shared across all three graphs, how many EPA FRS facilities (fiokg) coexist with SecureChain supply-chain participants and SUDOKN manufacturers, ranking industries by combined physical-plus-supply-chain footprint?
fiokg ↔ sudoknNAICS60For a manufacturing NAICS industry, list SUDOKN small/medium manufacturers (capabilities, certificates) alongside the EPA FRS facilities (fiokg) in that same industry - and, via fiokg's county/S2 location, where those facilities sit on the spatial hub.

Starting from EPA FRS facilities (fiokg) clustered in a given county via their S2/county links, which NAICS industries do they represent, and are there SUDOKN small/medium manufacturers with matching capabilities in those same NAICS codes for local sourcing?
medical-device-kg ↔ fiokgNAICS13For the NAICS industries FDA medical-device manufacturers are classified under, how many EPA-registered facilities does fiokg list in each?

How many of the NAICS codes medical-device-kg assigns to its manufacturers also classify facilities in fiokg?
medical-device-kg ↔ securechainkgNAICS12Which hardware manufacturers in securechainkg share a NAICS industry with FDA medical-device manufacturers, and what products do they make?

How many NAICS codes are used by both medical-device-kg manufacturers and securechainkg manufacturers, and which is missing?
securechainkg ↔ sudoknNAICS35For a manufacturing NAICS industry, list SUDOKN small/medium manufacturers (capabilities, certificates, capacity) and SecureChain supply-chain participants (software/hardware products and their vulnerabilities) in that same industry.

How many distinct SUDOKN manufacturers operate in each shared NAICS industry, and does the count of SecureChain participants (with known CVEs) in that same NAICS code rise or fall with it?
scales ↔ sudoknSUDOKN_company_IRI100Which SUDOKN manufacturers appear as parties in the most federal court cases, and how many products does SUDOKN list for each?

How many SUDOKN manufacturers does scales identify by SEC CIK, and how many case-party records do they account for?
securechainkg ↔ sudoknSUDOKN_industry_sector58Cross-reference the industry sectors served by SUDOKN manufacturers with the industry sectors of SecureChain supply-chain participants (e.g. which suppliers to the aerospace or automotive sector appear in both graphs).

Which SUDOKN-defined industry sector (aerospace, automotive, etc.) is served by the largest number of SecureChain supply-chain participants via suppliesToIndustry, and which manufacturers back it on the SUDOKN side?
securechainkg ↔ sudoknSUDOKN_product_IRI17,644Which manufacturers in Ohio make products with known vulnerabilities? (Novatech, Inc. — 6 products, CVE-2013-2821 and CVE-2013-2822; it is the only Ohio manufacturer on the bridge at all. Ohio is reached via sudokn:organizationLocatedIn/sudokn:locatedInState, not a predicate on the company node.)

Among small businesses (no more than 250 employees) whose products SecureChain tracks, which carry the most recorded vulnerabilities, and which carry none? (66 small manufacturers are on the bridge; only 10 carry any CVE — OptiLink Network leads with 12 on a single product — and 56 carry none, among them Coship Electronics and Dasan Networks. Needs sudokn:hasNumberOfEmployees on the SUDOKN side and sc:vulnerableTo on the securechainkg side, counted with OPTIONAL so zero-vulnerability firms survive. As first proposed this asked for small MODEM makers, but neither graph types or labels products as modems — SUDOKN product labels are model numbers and those firms carry no NAICS or product category — so the filter cannot be expressed against the data.)
climatemodelskg ↔ securechainkgclimatemodelskg Source IRI3Which climate models have the most vulnerable dependencies and the highest number of vulnerabilities? (CESM2, GFDL-ESM4 and GFDL-CM4 link through securechainkg sc:dependsOn to vulnerable PyPI packages and their CVEs.)

Given a specific vulnerable PyPI dependency (or its CVE) surfaced through securechainkg sc:dependsOn, which of CESM2, GFDL-ESM4, or GFDL-CM4 inherit that vulnerability?
medical-device-kg ↔ securechainkgcompany name195Which FDA-registered device establishments match a SecureChainKG manufacturer on both normalized name and ZIP, and what does SecureChainKG record about what they make and which industries they supply?

How many company names do medical-device-kg and SecureChainKG share, how many are ZIP-confirmed, and how many would the medical-device-kg x SUDOKN name bridge reach anyway?
medical-device-kg ↔ sudokncompany name364Which FDA-registered medical-device establishments are also profiled as US manufacturers in SUDOKN — and what process, material and capacity capability does SUDOKN add to a firm the FDA knows only as a registration record?

How many FDA device-establishment names match a SUDOKN manufacturer, and how many of those matches are confirmed by both graphs reporting the same ZIP?

Justice & Public Safety

KGsShared keyCountExamples
scales ↔ ruralkgNIBRS_offense_category37Rank the NIBRS offense categories that both drive SCALES federal charges and appear in ruralkg's rural crime-data codebook, showing federal charge volume and the NIBRS answer code for each.

For a NIBRS offense category tracked in ruralkg's rural crime-data codebook (e.g. Drug/Narcotic Violations), pull the matching SCALES federal charges under that OffenseUCRCode to see how the rural survey category translates into actual federal prosecutions.

Proteins

KGsShared keyCountExamples
biobricks-aopwiki ↔ nestkgUniProt1,376Which NeST cancer protein systems are enriched for proteins that AOP-Wiki names as molecular targets of adverse outcome pathways — i.e. which cancer systems are toxicologically perturbable?

How many AOP-Wiki UniProt key-event targets are members of the NeST protein-system map?
biobricks-aopwiki ↔ proknUniProt1,805Proteins acting as AOP molecular targets (AOP-Wiki) with their ProKN protein-centric annotations (domains, PTMs, marker genes, disease links).

Starting from ProKN proteins carrying disease links and PTMs, how many map by UniProt accession to AOP-Wiki molecular targets, and which adverse outcome pathways do they initiate?
biomarkerkg ↔ biobricks-aopwikiUniProt86Which clinical biomarker proteins are also AOP key-event targets, and which adverse outcome pathways involve them (toxicology meets clinical biomarkers)?

For a given AOP-Wiki adverse outcome pathway, which of its key-event target proteins (by UniProt) are validated clinical biomarkers in BiomarkerKB and for what disease?
biomarkerkg ↔ proknUniProt209For the clinical biomarker proteins a disease has in BiomarkerKB, what GO biological processes / molecular functions and pathways does ProKN annotate them with?

Across the 205 shared biomarker UniProt proteins, which GO biological processes and pathways does ProKN annotate most frequently, and do those processes cluster by the biomarker's disease category?
glygenkg ↔ biobricks-aopwikiUniProt756Which adverse outcome pathways have the most key-event target proteins that are glycosylated in GlyGen, and which targets are they?

How many of AOP-Wiki's UniProt-identified targets are glygenkg proteins, and how many of those have a glycosylation site record?
glygenkg ↔ biomarkerkgUniProt123Which clinical protein biomarkers carry the most distinct glycan structures in GlyGen (haptoglobin, lactotransferrin, PSA), at how many sites, and for which conditions are they biomarkers?

How many of BiomarkerKG's 245 UniProt protein analytes are glygenkg proteins, and how many have a site-level glycosylation record?
glygenkg ↔ ncipidkgUniProt1,348Which well-evidenced NCI-PID signalling interactions connect two proteins that both carry glycosylation sites in GlyGen (e.g. the insulin receptor and IRS1, NOTCH1 and NOTCH2)?

How many UniProt accessions do glygenkg and ncipidkg share, and how does that split between ncipidkg's own protein nodes and its owl:sameAs alias accessions?
glygenkg ↔ nestkgUniProt7,576Which NeST cancer protein systems have the largest share of members with a GlyGen glycosylation site, and are those sites on asparagine (N-linked) or on serine/threonine (O-linked)?

How many of glygenkg's 8,112 proteins are NeST proteins, and how many belong to a named NeST system?
glygenkg ↔ proknUniProt8,077For a glycoprotein such as the insulin receptor, which of GlyGen's glycosylated residues does ProKN's PTM layer also record, and what other modifications (phosphorylation, S-nitrosylation) does ProKN add on the same protein?

How many of glygenkg's 8,112 proteins have a ProKN record, and how many of its glycosylated residues match a ProKN glycosylation annotation at the same position?
ncipidkg ↔ proknUniProt2,493Signaling-pathway interaction proteins (NCI-PID) enriched with ProKN protein annotations.

Of the 2,493 shared UniProt proteins, which NCI-PID signaling hubs also carry a ProKN disease association or PTM annotation, flagging pathway nodes with therapeutic relevance?
nestkg ↔ biomarkerkgUniProt230Which clinically used protein biomarkers sit inside a NeST cancer protein system, and what else is in that system — i.e. which un-assayed proteins are the biomarker's system neighbours?

How many of BiomarkerKG's UniProt protein analytes are NeST proteins?
nestkg ↔ ncipidkgUniProt2,451Which NCI-PID signaling interactions run between two proteins of the SAME NeST system — i.e. where does curated pathway signaling agree with the data-driven NeST assembly?

How many NeST proteins take part in at least one NCI-PID interaction?
nestkg ↔ proknUniProt16,729What UniProt-level annotation — GO function, Reactome pathway, disease association — does ProKN add to the member proteins of a given NeST cancer protein system?

How many of nestkg's 16,767 NeST proteins carry a ProKN record?

Publications

KGsShared keyCountExamples
climatemodelskg ↔ nasa-gesdisc-kgDOI3,660For a climate-modeling paper in climatemodelskg (by DOI), does nasa-gesdisc-kg record that same publication among the works citing or using NASA Earth-science datasets - and which NASA datasets, instruments, or platforms does it connect to?

How many of climatemodelskg's papers are also in nasa-gesdisc-kg's publication set, joined on DOI?
glygenkg ↔ proknPubMed ID752For the papers that support the most glycosylation records in GlyGen, how many PTM annotations of which types does ProKN attribute to the same PubMed ID?

How many of the 1,516 papers GlyGen cites as glycosylation evidence are also cited in ProKN, by which kinds of record and for which modification types?
climatemodelskg ↔ nasa-gesdisc-kgauthor name (string; NOT an ORCID — see the entry's caveat)32,586At the COHORT level, how much overlap is there between the authors of climate-modeling papers (climatemodelskg) and the authors of papers citing NASA GES DISC Earth-observation datasets - i.e. is the climate-modeling community also the EO-data-using community?

How many climatemodelskg author names also appear as NASA GES DISC authors (note: a name match is NOT a person match - 11.3% of matched names resolve to more than one distinct ORCID)?

Social Determinants & Services

KGsShared keyCountExamples
spoke-okn → wikidata → biohealthMeSH→UMLS3For a County Health Rankings SDoH indicator spoke-okn tracks geographically (e.g. Social Vulnerability Index), what conditions does biohealth's literature graph link it to, reached through the MeSH->UMLS wikidata bridge?

Starting from a condition biohealth links in its literature graph (e.g. obesity), which County Health Rankings SDoH indicators does spoke-okn track geographically for it, reached backward through the UMLS->MeSH wikidata bridge?
spoke-okn ↔ biohealthconcept label (SNOMED preferred term ↔ UMLS concept name)89Which diseases does biohealth's literature graph link to a behavioural or environmental SDoH that spoke-okn catalogues (e.g. sedentary lifestyle, pollution), matched on the concept label?

Of the 89 SDoH concepts whose SNOMED label matches a biohealth UMLS concept name, how many carry disease associations in biohealth's literature graph, and which behavioural determinant links to the most conditions?
phaseskg ↔ biohealthconcept label (psychosocial / SDoH term ↔ UMLS concept name)8For the loneliness / social-isolation / social-withdrawal constructs the PHASES healthy-aging ontology defines, what conditions and determinants does biohealth's literature graph link them to?

For the 8 PHASES psychosocial constructs that resolve to a biohealth UMLS concept, which single construct (e.g. social isolation) surfaces the largest set of linked conditions and determinants in the literature graph?
dreamkg ↔ biohealthconcept label (social-service audience term ↔ UMLS concept name)21For the health conditions and social determinants that DREAM-KG provides services for, what does biohealth's clinical/SDoH graph link those concepts to?

Given a condition biohealth documents in its clinical/SDoH graph (e.g. diabetes), which DREAM-KG social services list that condition as an audience category, matched on the concept label?

Taxonomy

These are pairwise organism overlaps composed through the ubergraph hub, so each carries two materialized counts rather than one. exact_id = taxa with the identical NCBITaxon id on both sides (symmetric). clade_a_in_b / clade_b_in_a = how many of the first / second KG's taxa fall under the other's once expanded through ubergraph's subClassOf* hierarchy (directional). Clade membership is the more complete biological overlap and is often far larger when one KG records coarser taxa (genus) and the other finer ones (strain). Rows marked † are label-bridged (biohealth, which carries no NCBITaxon ids, matched by exact scientific name) — see the note below the table. Like every other domain, Examples carries two questions per row: the count question (what the exact_id / clade columns measure) and the science question the pair answers.

KGsexact_idclade A-in-B / B-in-AExamples
biobricks-aopwiki × gene-expression-atlas-okn78 / 8How many organisms do biobricks-aopwiki and gene-expression-atlas-okn share? exact_id=7 carry the identical NCBITaxon id; clade membership (8 / 8) expands through the ubergraph hierarchy.

For the organisms an Adverse Outcome Pathway is declared applicable to, does Expression Atlas actually profile gene expression in that same species - i.e. can an AOP's taxonomic applicability be grounded in real expression data?
biobricks-aopwiki × nde62164 / 961How many organisms do biobricks-aopwiki and nde share? exact_id=62 carry the identical NCBITaxon id; clade membership (164 / 961) expands through the ubergraph hierarchy.

Which organisms carrying an AOP taxonomic-applicability statement also appear in NIAID Data Ecosystem datasets, so a mechanistic toxicology pathway can be tied to available infectious-disease/host data for the same species?
biobricks-aopwiki × sawgraph710 / 85How many organisms do biobricks-aopwiki and sawgraph share? exact_id=7 carry the identical NCBITaxon id; clade membership (10 / 85) expands through the ubergraph hierarchy.

Are the species that AOPs are declared applicable to the same species SAWGraph samples for PFAS (fish and shellfish biota) - connecting mechanistic toxicology to measured environmental exposure in the same organism?
biobricks-aopwiki × spoke-genelab78 / 8How many organisms do biobricks-aopwiki and spoke-genelab share? exact_id=7 carry the identical NCBITaxon id; clade membership (8 / 8) expands through the ubergraph hierarchy.

Do the model organisms used in NASA GeneLab spaceflight experiments have Adverse Outcome Pathways declared applicable to them, so a spaceflight stressor response can be read against a known AOP?
gene-expression-atlas-okn × nde68 / 12How many organisms do gene-expression-atlas-okn and nde share? exact_id=6 carry the identical NCBITaxon id; clade membership (8 / 12) expands through the ubergraph hierarchy.

For the organisms represented in NIAID Data Ecosystem datasets, what baseline or differential gene expression does Expression Atlas supply for the same species?
gene-expression-atlas-okn × spoke-genelab88 / 8How many organisms do gene-expression-atlas-okn and spoke-genelab share? exact_id=8 carry the identical NCBITaxon id; clade membership (8 / 8) expands through the ubergraph hierarchy.

For a model organism flown in a NASA GeneLab spaceflight assay, what baseline tissue expression does Expression Atlas provide for the same species, as a ground control for the spaceflight response?
nde × sawgraph2634 / 86How many organisms do nde and sawgraph share? exact_id=26 carry the identical NCBITaxon id; clade membership (34 / 86) expands through the ubergraph hierarchy.

Which organisms appear both in NIAID Data Ecosystem datasets and in SAWGraph's environmental and biota samples - e.g. a sampled fish species that also carries pathogen/host data?
nde × spoke-genelab746 / 55How many organisms do nde and spoke-genelab share? exact_id=7 carry the identical NCBITaxon id; clade membership (46 / 55) expands through the ubergraph hierarchy.

Which of NASA GeneLab's spaceflight model organisms also have NIAID Data Ecosystem datasets, linking spaceflight omics to immune/infectious-disease resources for the same species?
nde × spoke-okn2323 / 33,601How many organisms do nde and spoke-okn share? exact_id=23 carry the identical NCBITaxon id; clade membership (23 / 33601) expands through the ubergraph hierarchy.

For an organism in a NIAID Data Ecosystem dataset, what does spoke-okn know about the same species (its genes, proteins and disease associations)? Note the large clade asymmetry: spoke-okn's taxonomy is far broader, so clade expansion pulls in 33,601 spoke-okn taxa.
nde × wildlifekn1757 / 339How many organisms do nde and wildlifekn share? exact_id=17 carry the identical NCBITaxon id; clade membership (57 / 339) expands through the ubergraph hierarchy.

Which wildlife species tracked in wildlifekn also appear in NIAID Data Ecosystem datasets - i.e. which monitored wild animals are also studied as zoonotic reservoirs or hosts?
sawgraph × wildlifekn33 / 4How many organisms do sawgraph and wildlifekn share? exact_id=3 carry the identical NCBITaxon id; clade membership (3 / 4) expands through the ubergraph hierarchy.

Which wildlife species monitored in wildlifekn are also sampled for PFAS contamination in SAWGraph - connecting wildlife occurrence and habitat to measured chemical exposure in the same species?
spoke-genelab × spoke-okn22 / 33,313How many organisms do spoke-genelab and spoke-okn share? exact_id=2 carry the identical NCBITaxon id; clade membership (2 / 33313) expands through the ubergraph hierarchy.

For a model organism used in a NASA GeneLab spaceflight experiment, what biomedical context does spoke-okn attach to the same species? Only 2 taxa match by exact id, but clade expansion through ubergraph reaches 33,313 spoke-okn taxa - so ALWAYS expand the clade here; an exact-id join badly understates this pair.
biohealth × biobricks-aopwiki †112 / 166—How many organisms do biohealth and biobricks-aopwiki share by name? biohealth is label-bridged (no NCBITaxon ids), so 112 of biobricks-aopwiki's 166 NCBITaxon organisms match a biohealth concept by exact scientific name (approximate lower bound; no clade expansion).

Which organisms named in biohealth's UMLS health concepts have an Adverse Outcome Pathway declared applicable to them? biohealth carries NO NCBITaxon ids, so this is an approximate scientific-name match - a lower bound, and not safe for exact-id reasoning.
biohealth × gene-expression-atlas-okn †6 / 8—How many organisms do biohealth and gene-expression-atlas-okn share by name? biohealth is label-bridged (no NCBITaxon ids), so 6 of gene-expression-atlas-okn's 8 NCBITaxon organisms match a biohealth concept by exact scientific name (approximate lower bound; no clade expansion).

For the organisms biohealth names as UMLS health concepts, does Expression Atlas profile expression in the same species? Name-bridged (no NCBITaxon ids on biohealth) - treat as an approximate lower bound.
biohealth × nde †1,052 / 1,808—How many organisms do biohealth and nde share by name? biohealth is label-bridged (no NCBITaxon ids), so 1052 of nde's 1808 NCBITaxon organisms match a biohealth concept by exact scientific name (approximate lower bound; no clade expansion).

Which organisms biohealth names as UMLS health concepts also appear in NIAID Data Ecosystem datasets - e.g. a named pathogen concept with real underlying data? Name-bridged, so this 1,052-organism overlap is an approximate lower bound.
biohealth × sawgraph †56 / 86—How many organisms do biohealth and sawgraph share by name? biohealth is label-bridged (no NCBITaxon ids), so 56 of sawgraph's 86 NCBITaxon organisms match a biohealth concept by exact scientific name (approximate lower bound; no clade expansion).

Which organisms biohealth names as UMLS health concepts are also sampled by SAWGraph for environmental contamination - linking a health concept to measured exposure in the same species? Name-bridged, so approximate.
biohealth × spoke-genelab †7 / 9—How many organisms do biohealth and spoke-genelab share by name? biohealth is label-bridged (no NCBITaxon ids), so 7 of spoke-genelab's 9 NCBITaxon organisms match a biohealth concept by exact scientific name (approximate lower bound; no clade expansion).

Do NASA GeneLab's spaceflight model organisms appear as organism concepts in biohealth's UMLS-keyed health graph? Name-bridged (biohealth has no NCBITaxon ids) - an approximate lower bound.
biohealth × spoke-okn †1,603 / 34,570—How many organisms do biohealth and spoke-okn share by name? biohealth is label-bridged (no NCBITaxon ids), so 1603 of spoke-okn's 34570 NCBITaxon organisms match a biohealth concept by exact scientific name (approximate lower bound; no clade expansion).

For an organism biohealth names as a UMLS health concept, what does spoke-okn record about the same species? The largest label-bridged overlap (1,603 of spoke-okn's 34,570 taxa match by scientific name) - but name-matched, so verify before asserting identity.

† Label-bridged. biohealth carries no NCBITaxon ids, so these overlaps are matched by exact scientific name, not NCBITaxon id. For these rows the count is label_match / partner's total taxa — how many of the partner KG's NCBITaxon organisms have a same-name biohealth concept, out of that KG's total — and the exact_id/clade semantics of the other rows do not apply. Name-based and conservative (misses synonyms and spelling variants), with no subClassOf* clade expansion.

For any pair, call get_join_strategy(kg_a, kg_b) to get the full recipe — predicates, roles, IRI-normalization snippet — or taxon_overlap(kg_a, kg_b) for runnable taxonomy skeletons.

Taxonomy: other organism vocabularies

KGsShared keyCountExamples
biobricks-mesh → babel → spoke-oknMeSH ↔ NCBITaxon4,078Through Babel, which MeSH organism branches do SPOKE-OKN's taxa fall under?

Same crosswalk, coverage angle: how many of SPOKE-OKN's taxa have a MeSH organism record, and of which kind?

Variants

KGsShared keyCountExamples
pankgraph ↔ biomarkerkgdbSNP rsID214For a pancreas-relevant variant in PanKgraph, is that same rsID used as a clinical susceptibility or diagnostic biomarker, and for which disease?

How many dbSNP variants are shared between PanKgraph and BiomarkerKG?
prokn ↔ biomarkerkgdbSNP rsID3,241For a variant BiomarkerKG uses as a clinical marker, what protein-level consequence does ProKN record — which protein, which residue change, and is it flagged as disease-associated?

How many of BiomarkerKG's 147,386 dbSNP variants have a UniProt natural-variant annotation in ProKN?
prokn ↔ pankgraphdbSNP rsID214For a pancreas-relevant variant in PanKgraph, does ProKN record a protein-level natural-variant annotation — and which protein and residue does it hit?

How many of PanKgraph's 19,448 dbSNP variants carry a UniProt natural-variant annotation in ProKN?