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Value data type (e.g. URI, URL, text, xsd:boolean):
CURIE (entity)
Example
subject_id
predicate_id
object_id
mapping_justification
mapping_chain_intermediate
comment
MONDO:123
skos:exactMatch
OMIM:111
semapv:MappingChaining
Orphanet:123
MONDO:222
skos:exactMatch
OMIM:321
semapv:MappingChaining
Orphanet:321|SCTID:123
mapping chain can hold multiple values to mean: hoped through multiple intermediates.
Description
Some ontologies such as GO and Mondo curate mappings based on mapping chaining. For example, from:
MONDO:123 --[skos:exactMatch]-->Orphanet:123 and
Orphanet:123 --[skos:exactMatch]-->OMIM:111
They deduce:
MONDO:123 --[skos:exactMatch]-->OMIM:111
The corresponding justification for this mapping in SSSOM is semapv:MappingChaining. Capturing such chains is very important. In Mondo and GO, mapping_chain_intermediate (in the above example, that would be Orphanet:123) are curated, using the oboInOwl:source property. This issue proposes to adopt this convention as a convenient and easily readable way to capture chain metdata.
Additional thoughts
I have been convinced through various discussions that this property is convenient, easy to understand and informative. However, for the sake of completeness I want to reveal that my preferred way of modelling this would have been to explicitly model mapping provenance by documenting the full path MONDO:123 --[skos:exactMatch]-->Orphanet:123--[skos:exactMatch]-->OMIM:111 in some way. Documenting the path as a string is a bit verbose (MONDO:123-skos:exactMatch->Orphanet:123-skos:exactMatch->OMIM:111 or whatever) and the more elegant way, referring to a mapping directly by identifier, is not possible because we decided to no have mapping_id in SSSOM so far (a globally unique identifier scheme for mappings would provide a huge burden to global integration and dependency on infrastructure which would make sssom much more heavyweight).
The text was updated successfully, but these errors were encountered:
Yes, this is exactly my argument againt this proposal. The predicates are collapsed. What this is saying is this:
"We traced a mapping chain through A,B,C and determined that this is sufficient to justify the current mapping".
Some information is lost, but it is maybe justifiable for the tersity gained. intermediates are very valuable evidence regardless of whether the mapping predicate was respected. Having the predicated would, however, make it even more explicit - at the cost of simplicity and readability.
Element id:
Value data type (e.g. URI, URL, text, xsd:boolean):
Example
Description
Additional thoughts
I have been convinced through various discussions that this property is convenient, easy to understand and informative. However, for the sake of completeness I want to reveal that my preferred way of modelling this would have been to explicitly model mapping provenance by documenting the full path
MONDO:123 --[skos:exactMatch]-->Orphanet:123--[skos:exactMatch]-->OMIM:111
in some way. Documenting the path as a string is a bit verbose (MONDO:123-skos:exactMatch->Orphanet:123-skos:exactMatch->OMIM:111
or whatever) and the more elegant way, referring to a mapping directly by identifier, is not possible because we decided to no havemapping_id
in SSSOM so far (a globally unique identifier scheme for mappings would provide a huge burden to global integration and dependency on infrastructure which would make sssom much more heavyweight).The text was updated successfully, but these errors were encountered: