colleenXu
commented
9 months ago Analysis of changes from biolink-model 3.5.3 -> 4.1.6
TDLR: Should be smooth process to update (CC Jackson @tokebe). While we can get the biolink-model module PR ready, I'm not sure if more changes are coming - I provided Sierra with some feedback, particularly the wording of the new predicates' inverses.
Note: I've been discussing issues with Sierra about biolink 4, which has led to changes and a moving goalpost of what biolink-model version to implement. Currently, we're on 4.1.6.
New chem/drug/treatment ↔️ disease/pheno predicates
promotes condition/condition promoted by: mixin, promoting condition's manifestation in the first place (opposite ofpreventative for condition)- note: inverse doesn't act as a mixin (see note below)
studied to treat/treated in studies by: report that a research study happened but not enough evidence of actually working- noting: inverse's wording was
studied for treatment within 4.1.0-4.1.3, but changed in 4.1.4
- noting: inverse's wording was
in clinical trials for/tested by clinical trials of(? asked about this inverse's wording): report clinical trial was performed to test potential of intervention to treat conditionin preclinical trials for/tested by preclinical trials of(? asked about this inverse's wording): report pre-clinical study was done to test potential of intervention to treat conditionbeneficial in models for/models demonstrating benefits for(? asked about this inverse's wording): reports of working treatment (alleviate, prevent, delay symptoms) in a model system for the diseaseapplied to treat/treatment applications from(? asked about this inverse's wording): report observations of human use in real world (not necessarily approved or effective). Can be from self-reporting (faers, aeolus) or off-label usetreats or applied or studied to treat/subject of treatment application or study for treatment by: mixin, should be able to use directly. Def - represent sources not clear about "treats", like text-mined statements. Now maps to SEMMEDDB treats.- note: inverse doesn't act as a mixin (see note below)
Adjusted chem/drug/treatment ↔️ disease/pheno predicates
ameliorates condition/condition ameliorated by: replacesameliorates/is ameliorated by. Def - can ameliorate symptoms, stable progression, cure condition. "beneficial/therapeutic for condition" (narrower than treats because it doesn't include prevention/reduce risk of future disease).preventative for condition/condition prevented by: replacesprevents/prevented by, with broad-mapping to SEMMEDDB prevents. Def - prophylactic for, preventing condition from manifesting in the first placepredisposes to condition/condition predisposed by: replacespredisposes/has predisposing factor, with broad-mapping to SEMMEDDB predisposes. slightly more specific thanpromotes condition, but basically the same? Def - "increases chances of condition coming to be"exacerbates condition/condition exacerbated by: replacesexacerbates/is exacerbated by. Def - worsens some or all aspects of condition, detrimental for condition. Mapped to SEMMEDDB COMPLICATEStreats/treated by: mixin, can still be used directly. Only use with strong supporting evidence (approved for this condition, passed phase 3, in phase 4, established treatment) or in the creative-mode prediction edges.- note: inverse doesn't act as a mixin (see note below)
contraindicated in(inverse is still the samehas contraindication): replacescontraindicated for. Def - shouldn't be applied as intervention with patients with condition because of risk for detrimental outcomes. Condition = biological entity because it's more general than disease/pheno - can include biological state/pregnancy and people taking warfarin/different meds being taken
Other
- "treats-refactor" edge-attributes:
clinical approval statusreplacesFDA approval status, goes with theClinicalApprovalStatusEnum(which has a hierarchy, replacesFDAApprovalStatusEnum)- add
max research phase, goes with theMaxResearchPhaseEnum(which has a hierarchy)
- affects BioThings semmeddb / suppKG x-bte annotation
STY:T167(substance, sbst) now mapped tochemical entitySTY:T190(Anatomical Abnormality, anab) now narrow-mapped to pheno (before it was mapped to disease)
splicingandmolecular interactionadded as possible terms for aspect qualifier (GeneOrGeneProductOrChemicalEntityAspectEnum)- infores catalog:
- deprecated quickgo
- using new human-goa (human gene-ontology annotations) rather than other infores?
- transcript, exon, coding sequence became children of biological entity, rather than nucleic acid entity
- not new: category including "ancestors" of the main class for the node
- new association types:
gene affects chemical association(w/ qualifier use)feature or disease qualifiers to entity mixin(reverse of existingentity to feature or disease qualifiers mixin)phenotypic feature to entity association mixin(reverse of existingentity to phenotypic feature association mixin)phenotypic feature to disease association
- doesn't affect us:
superclass_ofis labeled as inverse ofsubclass_of(subclass stays as the canonical one)severity qualifier,severity value,onset,onset qualifierdeprecated- adjusted predicate:
affects likelihood of/likelihood affected by: replacesaffects risk for/risk affected by? Def - object doesn't yet exist, but the actions/execution of subject impacts likelihood that object will come to be.- Not for statistical associations/correlations (which is the similar-sounding
associated with likelihood of/likelihood associated with) - different from
affects: the subject has an effect on the object which already exists
- Not for statistical associations/correlations (which is the similar-sounding
tokebe
[UPDATED]
We'll update to biolink-model 4.1.6:
Currently this is due in Dev/CI by 3/8 ~, with coordinated Translator requests to deploy to Test on 3/8~ CORRECTION: Chris Bizon in Architecture call 3/5 says not to deploy to Test.
What's involved: