callahantiff
commented
4 years ago @bill-baumgartner and @nicolevasilevsky hoping to get your feedback on my proposal for logically validating the mappings, which is described, with examples below.
I am also including @LEHunter so he knows my plan. The reason I am adding this last step is two fold: (1) the use of reasoners as logical validation was Melissa's idea (and hinted at by a an OHDSI reviewer), which I love and (2) the resulting mappings will compatible with PheKnowLator.
Background
We have generated mappings for several clinical domains (i.e. conditions, drug ingredients, and measurements). Each domain is mapped to a different set of ontologies and several types of mappings were created. Mappings that included more than a single ontology concept (many ontology concepts to one clinical concept) were constructed using owl:IntersectionOf, owl:UnionOf, or owl:ComplementOf (additional content on how each of these mappings of mappings will be RDF-ized is included at the top of this issue). The ontologies utilized for each domain and the different types of mappings that are generated are shown in the tables below:
Clinical Domains and Ontologies
| Clinical Domain | Ontologies |
|---|---|
| Conditions | HPO, MONDO |
| Drug Ingredients | CHEBI, PRO, NCBITaxon, VO |
| Measurements | HPO, UBERON, CL, CHEBI, NCBITaxon, PRO |
Mapping Categories
| Category | Definition |
|---|---|
| Automatic Exact - Concept | Exact label or synonym, dbXRef, or expert validated mapping @ concept-level; 1:1 |
| Automatic Exact - Ancestor | Exact label or synonym, dbXRef, or expert validated mapping @ concept ancestor-level; 1:1 |
| Manual Exact - Concept Similarity | Concept similarity score suggested mapping -- manually verified; 1:1 |
| Automatic Constructor - Concept | Exact label or synonym, dbXRef, cosine similarity, or expert validated mapping @ concept-level; 1:Many |
| Automatic Constructor - Ancestor | Exact label or synonym, dbXRef, cosine similarity, or expert validated mapping @ concept-level; 1:Many |
| Manual Constructor | Hand mapping created using expert suggested resources; 1:Many |
| Manual | Hand mapping created using expert suggested resources; 1:1 |
| UnMapped | No suitable mapping or not mapped type |
Mappings also have evidence, which varies according to the mapping type. An example is shown in the table below:
| Mapping category | Mapping Evidence |
|---|---|
| Automatic Exact - Concept | CONCEPT_DBXREF:snomed_68345001 OBO_LABEL-OMOP_CONCEPT_LABEL:apraxia OBO_LABEL-OMOP_CONCEPT_SYNONYM:apraxia CONCEPT_SIMILARITY:HP_0002186_1.0 |
Analysis Plan
For each ontology, I will create a new ontology class for all mappings including 2 or more ontology concepts (since single concepts already existing within each ontology).
Reasoner(s):
- Planning on using
Hermitfirst and if that does not work, thenELK - Run reasoner on each ontology before and adding new concepts
Output and Record Statistics:
For each run, I will record the following results (potentially by mapping type):
- Whether or not the reasoner finished. If not, record the reasons why and how the issues were fixed.
- The number of new inferences generated that include the mappings
ASK:
- [x] Do you think this plan makes sense?
Creating Release Version RDF
Once the validation described above is complete, I will create a more complex version of the mappings that spans all ontologies for a given mapping, rather than creating ontology-specific mappings. Creating mappings that span multiple ontologies will require some additional content not currently included in each mapping. I realize that there are many ways one could approach this, this is what I think is the easiest, quickest, and most clean/transparent. Each class created from this process with be done so under the OMOP2OBO namespace and, include the official OMOP concept label, synonyms, and have the OMOP concept and source codes assigned as DbXRefs (all of this we get for free from the mappings).
Steps:
1 - Merge all ontologies together (ontologies listed in table above)
2 - Create new OMOP2OBO classes (in OMOP2OBO namespace) for mappings that include 2 or more concepts (see details below for how to integrate mappings spanning multiple ontologies). DbXRefs and owl:equivalentClass added with the OMOP concept_id for all 1:1 mappings
3 - Add the following metadata for each mapping using ECO: Mapping Category and Mapping Evidence
Relations to Connect Mappings Spanning Multiple Ontologies
I'm also including the inverse for each relation.
CONDITIONS
Ontologies: HPO, MONDO
Relations: MONDO has phenotype HPO
DRUG INGREDIENTS
Ontologies: CHEBI, PRO, NCBITaxon, VO (every concept has a CHEBI annotation)
Relations:
CHEBIhas componentPROCHEBIin taxonNCBITaxonCHEBIhas componentVO
MEASUREMENTS
Ontologies: HPO, UBERON, CL, CHEBI, NCBITaxon, PRO (every concept has an HPO and UBERON annotation)
Relations:
HPOlocated inUBERONHPOcontainsorhas memberNCBITaxonHPOhas part that occurs inorhas componentCLHPOhas componentPROHPOhas componentCHEBI
ASK:
- [x] Do you think this plan makes sense?
- [x] Creating mappings that span multiple ontologies will require some additional content not currently included in each
- [x] Do you agree with the relations I used in the table above for connecting each of the ontologies for each clinical domain? When there was more than one good option I include "OR", please let me know what you think. These were tough.
nicolevasilevsky
bill-baumgartner
linikujp
Needed Scripts: Write a script that converts mappings into RDF
@nicolevasilevsky -- thank you for meeting with me a few weeks ago and confirming our approach looks reasonable. I am just documenting this here as an issue since it's work I still need to do.
Planned Approach
NOT() Details: Only occurs within the HP and only for Measurement and Drug domains class_IRI: https://github.com/callahantiff/omop2obo/obo/ext/OMOP_4021360 Class_Name: 'Skin appearance normal' Class Expression Syntax: not('Abnormality of the skin')
New Triples:
OR() Details: Only occurs within DOID and HP and only for the Condition domain class_IRI: https://github.com/callahantiff/omop2obo/obo/ext/OMOP_434473 Class_Name: 'Longitudinal deficiency of tibia AND/OR fibula' Class Expression Syntax:
('Abnormality of fibula morphology' or 'Abnormality of tibia morphology')New Triples:
AND() Details: Occurs within all ontologies and domains class_IRI: https://github.com/callahantiff/omop2obo/obo/ext/OMOP_434165 Class_Name: 'Abnormal cervical smear' Class Expression Syntax:
('Abnormal cell morphology' and 'Abnormality of the uterine cervix')New Triples:
AND()/OR() Details: Only occurs within DOID and HP and only for the Condition domain class_IRI: https://github.com/callahantiff/omop2obo/obo/ext/OMOP_77072 Class_Name: 'Joint effusion of ankle AND/OR foot' Class Expression Syntax:
New Triples:
AND()/NOT() Details: Only occurs within DOID and HP and only for the Condition domain class_IRI: https://github.com/callahantiff/omop2obo/obo/ext/OMOP_4120313 Class_Name: 'Non-diabetic disorder of endocrine pancreas' Class Expression Syntax:
'Abnormality of the pancreas' and not('has phenotype' some 'Diabetes mellitus')New Triples:
AND()/OR()/NOT() Details: Only occurs within DOID and HP and only for the Condition domain class_IRI: https://github.com/callahantiff/omop2obo/obo/ext/OMOP_435352 Class_Name: 'Periostitis without osteomyelitis, of the pelvic region and/or thigh' Class Expression Syntax:
New Triples: