Kent Shefchek

Consider annotation prop to distinguish disease grouping class vs disease entity

37

It would be useful if MONDO included a way to distinguish between a disease entity and a disease grouping. Currently the only way to do this is to check for...

In some cases it would be useful to have optional parameters that could be bound to an identifier when present, or have that line removed when the parameter is not...

We have a few places that use the START clause in cypher queries, this was removed in cypher 3.2, see https://neo4j.com/docs/cypher-manual/current/clauses/start/ https://github.com/SciGraph/SciGraph/blob/8a4d71/SciGraph-core/src/main/java/io/scigraph/internal/CypherUtil.java#L130 https://github.com/SciGraph/SciGraph/blob/8a4d7/SciGraph-core/src/main/java/io/scigraph/vocabulary/VocabularyNeo4jImpl.java#L317 https://github.com/SciGraph/SciGraph/blob/8a4d7/SciGraph-core/src/main/java/io/scigraph/owlapi/postprocessors/EdgeLabeler.java#L68

Store curies directly in neo4j, use rdf propertly labels as edge types

2

Right now SciGraph stores IRI's in Neo4J, and allows for a configuration of a curie map to be used in the service layer to convert between the two. However, querying...

Consider making isDefinedBy a node property

1

Currently all nodes are connected to their ontologies via a isDefinedBy. This is useful for quick provenance to the ontology node, which might also include metadata such as versionInfo. However,...

Limit by taxon for /vocabulary/autocomplete/{term}

3

It would be useful to be able to limit autocomplete results based on taxon ID or label. One use-case would be for searching for taxon specific phenotypes as an input...

For the cypher service, queries that have "nulls" return a 500 error, for example: [This works](https://scigraph-data.monarchinitiative.org/scigraph/cypher/execute?cypherQuery=++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%21%2A0..1%5D-%28feature%29-%5Bp%3ARO%3A0002200%7CRO%3A0002326%21%2A%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern1%27+as+pattern+++++++++UNION+++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%7CGENO%3A0000639%21%2A0..1%5D-%28feature%29%3C-%5B%3ABFO%3A0000051%21%2A%5D-%28genotype%3Agenotype%29-%5Bp%3ARO%3A0002200%7CRO%3A0002326%21%2A%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern2%27+as+pattern+++++++++UNION+++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%7CGENO%3A0000639%21%2A0..1%5D-%28feature%29%3C-%5B%3ABFO%3A0000051%21%2A%5D-%28genotype%3Agenotype%29%3C-%5B%3AGENO%3A0000222%7CRO%3A0001000%2A1..2%5D-%28person%29-%5Bp%3ARO%3A0002200%7CRO%3A0002326%21%2A%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern3%27+as+pattern+++++++++UNION+++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%5D-%28allele%29-%5B%3ABFO%3A0000051%21%2A%5D-%3E%28feature%29-%5B%3ARO%3A0002610%21%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern4%27+as+pattern&limit=10), but with .json [fails](https://scigraph-data.monarchinitiative.org/scigraph/cypher/execute.json?cypherQuery=++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%21%2A0..1%5D-%28feature%29-%5Bp%3ARO%3A0002200%7CRO%3A0002326%21%2A%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern1%27+as+pattern+++++++++UNION+++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%7CGENO%3A0000639%21%2A0..1%5D-%28feature%29%3C-%5B%3ABFO%3A0000051%21%2A%5D-%28genotype%3Agenotype%29-%5Bp%3ARO%3A0002200%7CRO%3A0002326%21%2A%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern2%27+as+pattern+++++++++UNION+++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%7CGENO%3A0000639%21%2A0..1%5D-%28feature%29%3C-%5B%3ABFO%3A0000051%21%2A%5D-%28genotype%3Agenotype%29%3C-%5B%3AGENO%3A0000222%7CRO%3A0001000%2A1..2%5D-%28person%29-%5Bp%3ARO%3A0002200%7CRO%3A0002326%21%2A%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern3%27+as+pattern+++++++++UNION+++++++++START+gene+%3D+node%3Anode_auto_index%28iri%3D%27http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F7145%27%29+++++++++MATCH+%28gene%29-%5Brel%3ARO%3AHOM0000017%7CRO%3AHOM0000020%5D-%28ortholog%29%3C-%5B%3AGENO%3A0000408%5D-%28allele%29-%5B%3ABFO%3A0000051%21%2A%5D-%3E%28feature%29-%5B%3ARO%3A0002610%21%5D-%3E%28object%3APhenotype%29+++++++++MATCH+%28ortholog%29-%5Btax%3ARO%3A0002162%5D-%3E%28taxon%29+++++++++RETURN+DISTINCT+++++++++ortholog.label+as+ortholog%2C+gene.label+as+gene%2C+object.label+as+phenotype+%2C+taxon.label+as+taxon%2C+++++++++%27pattern4%27+as+pattern&limit=10)

From @cmungall: - clarify which modules here are calculating natively vs calling owlsimX - general documentation

And other IRIs/curies where the behavior varies from other cases. For example in https://github.com/biolink/ontobio/blob/b47b05/ontobio/ontol.py#L401, parents() accepts subClassOf but not rdfs:subClassOf. Another improvement would be to have both work.

Add a new similarity API based on the interfaces defined here: https://github.com/biolink/ontobio/blob/master/ontobio/sim/api/interfaces.py This is blocked by https://github.com/monarch-initiative/monarch-devops/issues/124