| Cell types in abdominal organs |
ubergraph |
| Count how many publications use each dataset |
nasa-gesdisc-kg |
| Count the number of datasets by infectious agent in NDE. |
nde |
| Find a study related to influenza and links to other disease sources. |
ubergraph, nde |
| Find all diseases in NDE and the Mondo disease parent terms. |
federation |
| Find all gravel wells that connect to sand and gravel aquifers in Penobscot County, Maine. |
federation |
| Find all influenza related studies in NDE. |
nde |
| Find chemical compounds that treat rheumatoid arthritis. Return each compound's IRI and its label (name), ordered alphabetically by compound name, limited to the first 10 results. [easy] |
spoke-okn |
| Find compounds that downregulate genes associated with Alzheimer's disease. Return each gene's IRI and label (name) together with each compound's IRI and label (name), ordered alphabetically by gene name then compound name, limited to the first 10 results. [medium] |
spoke-okn |
| Find drugs that treat diseases strongly associated with a social determinant of health (odds ratio > 5 and Fisher's exact p-value < 0.001 for the SDoH-disease co-occurrence). Return the SDoH name, disease name, odds ratio, Fisher's p-value, and compound name, ordered by descending odds ratio, limited to the first 10 results. [hard] |
spoke-okn |
| Find genes associated with Alzheimer's disease |
prokn |
| Find genes expressed in pancreas acinar cells and regulating cell-matrix adhesion |
pankgraph, ubergraph |
| Find LINCS 1000 compounds that positively or negatively regulates at least one kinase gene, and is also perturbed in LINCS P100 |
prokn |
| Find NIBRS justice topics connected to NIBRS variables. |
ruralkg |
| Find NSDUH variables that explicitly mention a substance entity. |
ruralkg |
| Find phosphorylation sites that are likely to be downregulated by a perturbagen |
prokn |
| Find Properties and Relationships Associated with a Specific Gene(e.g., APOE) |
prokn |
| Find Properties and Relationships Associated with a Specific Protein(e.g., TP53) |
prokn |
| Find protein kinases in ProKN |
prokn |
| Find proteins associated with rare diseases by querying ProKN and Open Annotations Rare Disease (OARD) KG |
prokn |
| Find proteins encoded by genes associated with phenotypes of linked with factors such as Opioid Abuse influenced by SDoH |
prokn |
| Find proteins variants casually related to diseases linked with SDoH factors by querying ProKN and SPOKE KG |
prokn |
| Find proteins variants causally related to rare diseases by querying ProKN and Open Annotations Rare Disease (OARD) KG |
prokn |
| Find RuralKG treatment providers that offer telemedicine or telehealth therapy. |
ruralkg |
| Find science keywords most frequently cited by publications |
nasa-gesdisc-kg |
| Find science keywords most frequently cited by publications, matching labels against GCMD identifiers on Wikidata |
federation |
| Find the human ortholog gene(s) of the model-organism gene with symbol "Adh1". Return each human gene's IRI and symbol, ordered alphabetically by symbol. [easy] |
spoke-genelab |
| Get 10 locations from the knowledge graph, their assoicated super locations, sub locations, and s2 cells |
sockg |
| Get all Harvest Fraction Samples and their corresponding attributes (date, expUnit, treatmentId, crop, growth stage, etc.) |
sockg |
| Get all non-NAN values from the class BiomassCarbohydrate and their associated metadata (ExpUnit, date, crop, etc.) |
sockg |
| Get all organisms associated with protein groups (via UniProt) |
evoweb, ubergraph |
| Get all sites and what field they are contained in along with their postal codes. |
sockg |
| Get all Soil Biological Samples and their corresponding attributes (date, lower and upper depth, expUnit, etc.) |
sockg |
| Get all Water Data Samples and their corresponding attributes (date, expUnit, treatmentId, Runoff, growth stage, etc.) |
sockg |
| Get disease-phenotype associations in OARD in concordance with Ubergraph (disease)-[disease has feature]-(phenotypic feature) |
oard-kg |
| Get diseases most strongly associated with a list of phenotypes |
oard-kg |
| Get diseases most strongly associated with a phenotype (Increased total monocyte count) |
oard-kg |
| Get phenotypes most strongly associated with a disease (Marfan syndrome) |
oard-kg |
| How many sand and gravel aquifers spatially intersect each Maine town? |
federation |
| In study OSD-244, find model-organism genes that are significantly differentially expressed (FDR-adjusted p-value < 0.05) between spaceflight and matched ground control for the 60-day cohort. Consider only assays that directly contrast a Space Flight test group against a Ground Control reference group, oriented so the log2 fold change reflects spaceflight relative to ground control, and exclude reverse-direction duplicates. The two compared groups must be matched on biological material and on every experimental factor except the one distinguishing spaceflight from ground control: each non-spaceflight factor present on one side must also be present on the other, in both directions, so any assay whose groups differ on an additional covariate is rejected. Return each gene's IRI and symbol with the log2 fold change and adjusted p-value, ordered by ascending adjusted p-value and then by gene IRI to break ties, limited to the first 10 results. [medium] |
spoke-genelab |
| List 100 substances in RURAL-KG |
ruralkg |
| List All Diseases and Their Names and Sources |
prokn |
| List all labeled interactions |
ncipidkg |
| List all proteins with labels |
ncipidkg |
| List all resources in NDE and count the number of studies in each resource. |
nde |
| List assays by source from InvitroDB that are found in both ICE and ToxCast |
biobricks-ice |
| List datasets and their science keywords |
nasa-gesdisc-kg |
| List distinct judges |
scales |
| List neighbors of HDAC1 protein |
ncipidkg |
| List publications and the datasets they use |
nasa-gesdisc-kg |
| List publications by year and title |
nasa-gesdisc-kg |
| List RuralKG counties in high-rurality RUCC categories 7 through 9. |
ruralkg |
| List RuralKG mental health service categories and their service counts. |
ruralkg |
| List RuralKG treatment providers with GNIS service-location identifiers. |
ruralkg |
| List SCALES ontology event labels |
scales |
| List services that are available on Saturday or Sunday |
dreamkg |
| List services that are provided in more than one language |
dreamkg |
| List software dependencies of versions of ffmpeg |
securechainkg |
| List the names of chemical entities and optionally their CAS RN and DSSTOXSID if available |
biobricks-ice |
| List things and their labels |
federation |
| List vulnerabilities in versions of ffmpeg |
securechainkg |
| Processes that output glucose |
ubergraph |
| Publications using a specific dataset, matching identifiers against DOIs on Wikidata |
federation |
| Retrieve all Census Bureau county subdivisions for Clare County, Michigan. |
spatialkg |
| Retrieve all chemical manufacturing facilities (NAICS code 325) and their 6-digit industry code. |
fiokg |
| Retrieve all counties for New Mexico (FIPS = 35) |
spatialkg |
| Retrieve all flowlines named 'Illinois River |
hydrologykg |
| Retrieve all solid waste landfills (NAICS Industry Code 562212) in the state of Georgia (FIPS code 13) and their name and the town they are located in. |
federation |
| Retrieve the NAICS Industry classifications of the facility with FRS ID 110000428662. |
fio-kg |
| Scientific articles in Wikidata about a cell type that Ubergraph says is part of the abdomen |
ubergraph, wikidata |
| Show 100 triples |
federation |
| What is the adrenal gland part of? |
ubergraph |
| What is the average change in SOC stock (kg C ha-1 yr-1) in 0-30 cm soils? (5, 10, 15…)? This would require using equation above for Year 0 (=baseline year or first year of collection) and Year 5, 10, 15, etc…, then calculating the difference/# years. a. For each year, Delta SOC stock (kg ha-1) = Delta SOC stock (kg ha-1)yearX- Delta SOC stock (kg ha-1)baseline b. Average the Delta SOC stock (0-30cm) for the treatments of interest. |
sockg |
| What is the average increase in temperature from the first sample of an experimental unit for ghg flux samples. |
sockg |
| What is the average SOC stock (kg C ha-1) for 0-30 cm? a. For each field replicate sampled during the experiment (date) calculate SOC stock. * SOC stock (kg ha-1)= Organic C (g C/kg soil) * Bulk Density(g/cm3) * Soil depth(cm) * 100. 1ha=10,000m2 b. For each field replicate, sum kg ha-1 for all depth layers (0-5cm, 5-10cm, 10-30cm). If multiple soil increments measured between 0-30 cm, equation is the summation of calculation above for each increment. c. Average the SOC stock (0-30cm) for the treatments of interest. |
sockg |
| What is the average SOC Stock of available states |
sockg |
| What is the SOC stock, based on treatment Id, and what are the values used to find the SOC stock for each instance for GAJPCSR1_F1H2 on 1998-04-20? |
sockg |
| What is the Soil Organic Carbon (SOC) stock for each layer in experimental unit NDMAH3_T on 2008-04-04? Include Experimental Unit ID, Treatment ID, Date of Values, number the values used to calculate SOC stock, and the SOC stock value. |
sockg |
| What surface water bodies are downstream from a particular S2 cell? |
hydrologykg |
| Where is each field in the United States located (country, state) |
sockg |
| Which fields and their associated sites are located in Texas, and in which city are these fields found? Return the Field ID, Site ID, and Location with the struct (city, state abbreviation). |
sockg |
| Which management treatment (N rate, crop rotation, tillage, residue management) results in the greatest increase of SOC stocks (0-30cm, or o-100cm) after 15 years in rainfed sites? In irrigated treatments? This asks to rank the delta SOC stock calculations above. |
sockg |
| Which samples have a carbon concentration greater than or equal to 475 gC/kg? What additional information about these samples might help explain why their carbon concentration is so high? Include Unique ID, Treatment ID, Crop(s) used at Field, Plant Fraction use, Carbon Concentration value in your response. |
sockg |
| Which water bodies are called 'Great Pond' or 'Long Pond' and where are they located? |
federation |
| Who worked on the agcros dataset, what was their role, and what field did they work on? |
sockg |
| Within NASA study OSD-48 (Rodent Research 1), find mouse genes (and their human orthologs) that show BOTH a transcriptomic and an epigenomic response to spaceflight: down-regulated in expression (log2 fold change < −1 and FDR-adjusted p-value < 0.05) AND linked to a differentially methylated genomic region (methylation q-value < 0.05). Draw the two signals from two distinct assays, one differential-expression assay and one differential-methylation assay, that each compare the Space Flight condition against the Ground Control condition. Enforce experimental-condition consistency on the other (non-spaceflight) factors, not just on spaceflight status and biological material: within each assay, the two compared groups must have identical non-spaceflight experimental factors, so the groups differ only in spaceflight status and across the two assays, the differential-expression assay and the differential-methylation assay must use the same biological material and the same non-spaceflight factor value as each other. Return each human gene's IRI and symbol, the mouse gene symbol, the expression log2 fold change, the expression FDR-adjusted p-value, the methylation difference (percent), and the methylation q-value (and the shared condition factor), ordered by ascending log2 fold change, then ascending expression adjusted p-value, then human gene symbol, then human gene IRI, then mouse gene symbol, then methylation q-value, then ascending methylation difference, then methylation region IRI. [hard] |
spoke-genelab |