biolink-model
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biolink
Schema and generated objects for biolink data model and upper ontology
CTDbase.org has some nice data on exposures and diseases. The exposure is in terms of a chemical (identified by mesh). So the relationship is something like: (chemical) -[exposure to is...
This issue is in reference to DrugMechDB conversion to biolink, see issue #314 Similar to issue #316, `Chemical ELEVATED_IN Disease` is present in DrugMechDB. The meaning of this does not...
This issue is in reference to DrugMechDB conversion to biolink, see issue #314 One relationship in DrugMechDB is `Chemcial REDUCED_IN Disease`. This relationship implies that a reduced concentration of a...
**Is your feature request related to a problem? Please describe.** See the DisGeNET associations (OWL classes) hierarchy [here](https://www.disgenet.org/dbinfo#section5) and [here](https://www.ebi.ac.uk/ols/ontologies/sio/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000983&viewMode=All&siblings=false) for Gene -> Disease and Variant -> Disease relationships In...
**Is your feature request related to a problem? Please describe.** The issue is picking a predicate for drugbank descriptions of genes/proteins that are linked to chemicals (keywords like enzyme, carrier,...
- [ ] Document how to make Gene->Biological Process triples (which predicate to use when). - [ ] Where should 'function_of' be mapped in the model
 - [biolink:negatively_regulates](https://w3id.org/biolink/vocab/negatively_regulates) EquivalentTo [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) (most probable) 0.8 - [biolink:negatively_regulates](https://w3id.org/biolink/vocab/negatively_regulates) ProperSuperClassOf [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630) (most probable) 0.8 - [biolink:process_negatively_regulates_process](https://w3id.org/biolink/vocab/process_negatively_regulates_process) ProperSubClassOf [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) 0.06 - [biolink:acts_upstream_of_negative_effect](https://w3id.org/biolink/vocab/acts_upstream_of_negative_effect) EquivalentTo [acts upstream of,...
**Question:** What is the best biolink mapping for "endogenous". we are using this attribute in an edge that has a predicate of "biolink:decreases_activity_of". (After you create this ticket, you are...
Text mining provider would like to use 'has participant' and 'actively involved in' predicates (because they are canonical) to make gene-to-goterm associations. Two issues to resolve: 1) This might be...
**Is your feature request related to a problem? Please describe.** We are interested in adding information on histone post-translational modifications to our graphs. There are various things that we'd like...