kevinschaper
commented
5 months ago Purely looking at category counts:
sqlite3 -markdown monarch-kg.db "select category, count(*) from nodes where provided_by = 'phenio_nodes' group by 1 order by 2 desc"| category | count(*) |
|---|---|
| biolink:PhenotypicFeature | 123272 |
| biolink:BiologicalProcessOrActivity | 38774 |
| biolink:GrossAnatomicalStructure | 28388 |
| biolink:Disease | 27697 |
| biolink:Cell | 18762 |
| biolink:NamedThing | 18613 |
| biolink:AnatomicalEntity | 11665 |
| biolink:CellularComponent | 5283 |
| biolink:MolecularEntity | 4582 |
| biolink:BiologicalProcess | 3133 |
| biolink:MacromolecularComplex | 2131 |
| biolink:MolecularActivity | 1311 |
| biolink:Protein | 1117 |
| biolink:CellularOrganism | 955 |
| biolink:PhenotypicQuality | 744 |
| biolink:Pathway | 662 |
| biolink:Vertebrate | 391 |
| biolink:Virus | 320 |
| biolink:BehavioralFeature | 297 |
| biolink:LifeStage | 238 |
| biolink:PathologicalProcess | 231 |
| biolink:ChemicalEntity | 221 |
| biolink:Drug | 101 |
| biolink:OrganismTaxon | 93 |
| biolink:SmallMolecule | 70 |
| biolink:SequenceVariant | 70 |
| biolink:InformationContentEntity | 23 |
| biolink:NucleicAcidEntity | 18 |
| biolink:EvidenceType | 16 |
| biolink:GeographicExposure | 14 |
| biolink:RNAProduct | 12 |
| biolink:Transcript | 6 |
| biolink:Plant | 4 |
| biolink:Fungus | 4 |
| biolink:ProteinFamily | 3 |
| biolink:PopulationOfIndividualOrganisms | 3 |
| biolink:Invertebrate | 3 |
| biolink:Dataset | 3 |
| biolink:WebPage | 2 |
| biolink:Treatment | 2 |
| biolink:Study | 2 |
| biolink:RegulatoryRegion | 2 |
| biolink:Publication | 2 |
| biolink:ProteinDomain | 2 |
| biolink:Patent | 2 |
| biolink:MicroRNA | 2 |
| biolink:MaterialSample | 2 |
| biolink:Mammal | 2 |
| biolink:IndividualOrganism | 2 |
| biolink:Human | 2 |
| biolink:Haplotype | 2 |
| biolink:Genotype | 2 |
| biolink:Genome | 2 |
| biolink:GeneticInheritance | 2 |
| biolink:Gene | 2 |
| biolink:Exon | 2 |
| biolink:EnvironmentalFeature | 2 |
| biolink:ConfidenceLevel | 2 |
| biolink:ChemicalExposure | 2 |
| biolink:Agent | 2 |
| biolink:Activity | 2 |
| biolink:Zygosity | 1 |
| biolink:TranscriptionFactorBindingSite | 1 |
| biolink:StudyVariable | 1 |
| biolink:Snv | 1 |
| biolink:SiRNA | 1 |
| biolink:ReagentTargetedGene | 1 |
| biolink:ProcessedMaterial | 1 |
| biolink:Procedure | 1 |
| biolink:Polypeptide | 1 |
| biolink:PhenotypicSex | 1 |
| biolink:OrganismalEntity | 1 |
| biolink:NoncodingRNAProduct | 1 |
| biolink:GenotypicSex | 1 |
| biolink:Event | 1 |
| biolink:EnvironmentalProcess | 1 |
| biolink:DrugExposure | 1 |
| biolink:DiagnosticAid | 1 |
| biolink:DatasetDistribution | 1 |
| biolink:CodingSequence | 1 |
| biolink:ChemicalMixture | 1 |
| biolink:CellLine | 1 |
| biolink:BiologicalSex | 1 |
| biolink:BiologicalEntity | 1 |
| biolink:Bacterium | 1 |
| biolink:Attribute | 1 |
| biolink:Article | 1 |
| biolink:AccessibleDnaRegion | 1 |
caufieldjh
While checking on an older issue, I found that we're getting "gene" nodes from phenio:
We likely want to have either an include or exclude filter on either the contents of kg-phenio or what parts of kg-phenio are imported into monarch-kg.