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Re-map node and edge properties to Biolink slots #3

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caufieldjh opened this issue Feb 14, 2022 · 0 comments
Open

Re-map node and edge properties to Biolink slots #3

caufieldjh opened this issue Feb 14, 2022 · 0 comments

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@caufieldjh
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The full extent of node and edge properties used in Biolink do not explicitly map to Biolink property slots, but can be mapped - probably a good use case for SSSOM. An example - nodes and edges from the Asthma Ontology:

$ head AO_2_nodes.tsv
id      category        name    provided_by     :http://data.bioontology.org/metadata/def/mappingLoom   :http://data.bioontology.org/metadata/def/prefLabel     :http://data.bioontology.org/metadata/prefixIRI comment type
http://childhealthservicemodels.eu/asthma#MOCHA_0300    biolink:NamedThing      national asthma program tmps_d74ivz     nationalasthmaprogram   national asthma program asthma:MOCHA_0300               owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000082   biolink:NamedThing      management      tmps_d74ivz     management      management      asthma:MOCHA-Asthma_000082              owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000056     biolink:NamedThing      extrinsic asthma with status asthmaticus        tmps_d74ivz     extrinsicasthmawithstatusasthmaticus    extrinsic asthma with status asthmaticus   asthma:MOCHA-ADHD_000056         owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000000     biolink:NamedThing      general tmps_d74ivz     general general asthma:MOCHA-ADHD_000000                owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000162   biolink:NamedThing      passive smoking exposure        tmps_d74ivz     passivesmokingexposure  passive smoking exposure        asthma:MOCHA-Asthma_000162              owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000063     biolink:NamedThing      environmental   tmps_d74ivz     environmental   environmental   asthma:MOCHA-ADHD_000063                owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000052     biolink:NamedThing      intrinsic asthma with status asthmaticus        tmps_d74ivz     intrinsicasthmawithstatusasthmaticus    intrinsic asthma with status asthmaticus   asthma:MOCHA-ADHD_000052         owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000283   biolink:NamedThing      primary care asthma register    tmps_d74ivz     primarycareasthmaregister       primary care asthma register    asthma:MOCHA-Asthma_000283         owl:Class
http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000077   biolink:NamedThing      other   tmps_d74ivz     other   other   asthma:MOCHA-Asthma_000077              owl:Class

For one, the provided_by isn't really informative since it's just using the name of the temp file used during transformation.
The :http://data.bioontology.org/metadata/prefix prefix slots aren't explicitly Biolink-compatible.
And the edges:

subject predicate       object  relation        knowledge_source
http://childhealthservicemodels.eu/asthma#MOCHA_0300    :http://data.bioontology.org/metadata/def/mappingSameURI        http://childhealthservicemodels.eu/asthma#MOCHA_0300    :http://data.bioontology.org/metadata/def/mappingSameURI   tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA_0300    biolink:subclass_of     http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000082   rdfs:subClassOf tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000082   :http://data.bioontology.org/metadata/def/mappingSameURI        http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000082   :http://data.bioontology.org/metadata/def/mappingSameURI    tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000082   biolink:subclass_of     http://childhealthservicemodels.eu/asthma#MOCHA-EPI_0000037     rdfs:subClassOf tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000056     :http://data.bioontology.org/metadata/def/mappingSameURI        http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000056     :http://data.bioontology.org/metadata/def/mappingSameURI    tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000056     biolink:subclass_of     http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000000     rdfs:subClassOf tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000000     :http://data.bioontology.org/metadata/def/mappingSameURI        http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000000     :http://data.bioontology.org/metadata/def/mappingSameURI    tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA-ADHD_000000     biolink:subclass_of     http://childhealthservicemodels.eu/asthma#MOCHA-EPI_0000033     rdfs:subClassOf tmps_d74ivz
http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000162   :http://data.bioontology.org/metadata/def/mappingSameURI        http://childhealthservicemodels.eu/asthma#MOCHA-Asthma_000162   :http://data.bioontology.org/metadata/def/mappingSameURI    tmps_d74ivz

This is more of a matter of mapping predicates - biolink:subclass_of is fine but :http://data.bioontology.org/metadata/def/mappingSameURI can be replaced (and in these cases, it isn't even doing anything)

@caufieldjh caufieldjh added the Bioportal Issues specific to Bioportal label Feb 14, 2022
@caufieldjh caufieldjh removed the Bioportal Issues specific to Bioportal label Mar 7, 2022
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