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Additional EFO xref context from axioms #19

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Oct 5, 2023
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Additional EFO xref context from axioms #19

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e93019a
Add mapping properties and sources SPARQL queries
Sep 27, 2023
b80eef8
rename sources to xref_sources
Oct 2, 2023
3d7167e
save xref sources and mapping properties as output, add order by in m…
Oct 4, 2023
5cc274a
add curie normalization
Oct 4, 2023
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28 changes: 28 additions & 0 deletions nxontology_data/efo/queries/mapping_properties.rq
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Once the queries are done, what would be the next steps? How this data should be represented in the output?

We can save the tables as output and/or we can include in the nxontology. We'll have to decide how we want to represent this information as node data in networkx. Doing so is tricky because we have to decide to what extent users will want access to rawer forms versus a more consolidated but opinionated format.

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@dhimmel How about saving the table in the output for now, so that users can access this data? We could create a follow up issue to discuss how we can represent this information as node data in networkx.

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How about saving the table in the output for now

Sounds good.

Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
PREFIX mondo: <http://purl.obolibrary.org/obo/mondo#>
PREFIX efo: <http://www.ebi.ac.uk/efo/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT ?efo_id ?xref_id ?mapping_property_id ?efo_uri ?xref_uri ?mapping_property_uri
WHERE {
VALUES ?mapping_property_uri {mondo:closeMatch mondo:exactMatch skos:mappingRelation skos:closeMatch skos:exactMatch skos:broadMatch skos:narrowMatch skos:relatedMatch}

?efo_uri rdf:type owl:Class .
?efo_uri ?mapping_property_uri ?xref_uri


BIND( REPLACE( STR(?efo_uri), "^http.+/([^:]+)_(.+)$", "$1:$2" ) AS ?efo_id )
BIND( REPLACE( STR(?xref_uri), "^http.+/([^:]+)_(.+)$", "$1:$2" ) AS ?xref_id_dirty )
BIND(
COALESCE(
IF( STRSTARTS( ?xref_id_dirty, "http://identifiers.org" ), REPLACE( ?xref_id_dirty, "^http.*/(.+)/(.+)$", "$1:$2" ), ?error ),
IF( STRSTARTS( ?xref_id_dirty, "http://linkedlifedata.com/resource/umls/id" ), REPLACE( ?xref_id_dirty, "^http.*/(.+)$", "UMLS:$1" ), ?error ),
IF( STRSTARTS( ?xref_id_dirty, "http://purl.bioontology.org/ontology/ICD10CM" ), REPLACE( ?xref_id_dirty, "^http.*/(.+)$", "ICD10CM:$1" ), ?error ),
IF( STRSTARTS( ?xref_id_dirty, "https://icd.who.int/browse10/2019/en#" ), REPLACE( ?xref_id_dirty, "^http.*/(.+)$", "ICD10:$1" ), ?error ),
IF( STRSTARTS( ?xref_id_dirty, "https://omim.org/entry" ), REPLACE( ?xref_id_dirty, "^http.*/(.+)$", "OMIM:$1" ), ?error ),
IF( STRSTARTS( ?xref_id_dirty, "https://omim.org/phenotypicSeries" ), REPLACE( ?xref_id_dirty, "^http.*/PS(.+)$", "OMIMPS:$1" ), ?error ),
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All these special cases are a bit annoying to maintain, but great work figuring them out. Was it just an iterative process of figuring out which URIs are not handled?

One option would be to save the URI to CURIE conversion for post-processing in python with bioregistry.curie_from_iri or curies.

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Was it just an iterative process of figuring out which URIs are not handled?

Yes, this was an iterative process

One option would be to save the URI to CURIE conversion for post-processing in python with bioregistry.curie_from_iri or curies.

Thanks for the tip, this would be better if we can do it like that.

I used curies.get_bioregistry_converter to get the converter for URIs. However, there are some differences how curies maps URIs compared to how I mapped them. Here are some examples:

  • orphanet:99022 vs obo:orphanet_99022 URI: http://purl.obolibrary.org/obo/Orphanet_99022. Should we replace obo:orphanet_ with orphanet:?
  • orphanet:98813 vs orphanet.ordo:98813 URI: http://www.orpha.net/ORDO/Orphanet_98813 I guess we can replace orphanet.ordo with orphanet akin to

    nxontology-data/nxontology_data/utils.py

    Lines 84 to 88 in c7b1429

    if collapse_orphanet and prefix.lower() == "orphanet.ordo":
    # In EFO, all orphanet.ordo terms existed in orphanet.
    # The consistency of using a single prefix will help with mapping.
    # https://github.com/biopragmatics/bioregistry/issues/187#issuecomment-1706308305
    prefix = "Orphanet"
  • omimps:203655 vs omim.ps:203655 URI: https://omim.org/phenotypicSeries/PS203655 . Should we replace omim.ps with omimps?

There is also a missing uri_prefix http://purl.bioontology.org/ontology/ICD10CM/ for ICD10CM. The add_prefix method for adding prefixes lacks merge option in the version we use. Would it be safe to update the curies version?

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  • Should we replace obo:orphanet_ with orphanet:?

Yes. It's nice that curies handles that.

For orphanet, we can replace orphanet.ordo after normalization.

omim.ps is the correct normalized prefix.

Ideal is you call normalize_parsed_curie on the output of curies.get_bioregistry_converter so we get consistently formatted CURIES everywhere.

?xref_id_dirty
) AS ?xref_id
)
BIND( REPLACE( STR(?mapping_property_uri), "^http://purl\\.obolibrary\\.org/obo/mondo#(.+)$", "mondo:$1" ) AS ?mapping_property_id )
BIND( REPLACE( STR(?mapping_property_id), "^http://www\\.w3\\.org/2004/02/skos/core#(.+)$", "skos:$1" ) AS ?mapping_property_id )
}
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Can you reply to this comment with the head of the output table?

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efo_id xref_id mapping_property_id efo_uri xref_uri mapping_property_uri
MONDO:0000044 meddra:10060873 mondo:closeMatch http://purl.obolibrary.org/obo/MONDO_0000044 http://identifiers.org/meddra/10060873 http://purl.obolibrary.org/obo/mondo#closeMatch
MONDO:0000050 meddra:10035083 mondo:closeMatch http://purl.obolibrary.org/obo/MONDO_0000050 http://identifiers.org/meddra/10035083 http://purl.obolibrary.org/obo/mondo#closeMatch
MONDO:0000088 meddra:10044701 mondo:closeMatch http://purl.obolibrary.org/obo/MONDO_0000088 http://identifiers.org/meddra/10044701 http://purl.obolibrary.org/obo/mondo#closeMatch
MONDO:0000088 meddra:10058084 mondo:closeMatch http://purl.obolibrary.org/obo/MONDO_0000088 http://identifiers.org/meddra/10058084 http://purl.obolibrary.org/obo/mondo#closeMatch
MONDO:0000127 meddra:10063361 mondo:closeMatch http://purl.obolibrary.org/obo/MONDO_0000127 http://identifiers.org/meddra/10063361 http://purl.obolibrary.org/obo/mondo#closeMatch

17 changes: 17 additions & 0 deletions nxontology_data/efo/queries/sources.rq
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Let's rename to xref_sources.rq

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Ok

Original file line number Diff line number Diff line change
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>

SELECT ?efo_id ?xref ?axiom_source
WHERE {
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I wonder if there are cases of xrefs that don't have any axioms, i.e. things matched by

nxontology-data/nxontology_data/efo/queries/xrefs.rq

Lines 28 to 29 in c7b1429

?source_efo_uri rdf:type owl:Class.
?source_efo_uri oboInOwl:hasDbXref ?xref_raw.

We could do this match first and then make the axiom match OPTIONAL. Or we could decide this query is only for getting xref sources and we don't care about anything without a source.

Questions:

  1. Do all oboInOwl:hasDbXref triples have corresponding axioms?
  2. Do all axioms with owl:annotatedProperty oboInOwl:hasDbXref have corresponding oboInOwl:hasDbXref triples?

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I wonder if there are cases of xrefs that don't have any axioms, i.e. things matched by

There are cases like that, for example MONDO:0004947 in EFO:0000094 and ICD10:O35 in EFO:0009682 don't have axioms.

We could do this match first and then make the axiom match OPTIONAL. Or we could decide this query is only for getting xref sources and we don't care about anything without a source.

I think that this query should be only for getting xref sources

?axiom rdf:type owl:Axiom.
?axiom owl:annotatedSource ?source.
?axiom owl:annotatedProperty oboInOwl:hasDbXref.
?axiom owl:annotatedTarget ?xref.

OPTIONAL { ?axiom oboInOwl:source ?axiom_source }.

BIND( REPLACE( STR(?source), "^http.+/([^:]+)_(.+)$", "$1:$2" ) AS ?efo_id )
}

GROUP BY ?efo_id ?xref ?axiom_source
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Can you reply to this comment with the head of the output table?

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efo_id xref axiom_source
CHEBI:100241 Beilstein:3568352 Beilstein
CHEBI:100241 CAS:85721-33-1 ChemIDplus
CHEBI:100241 CAS:85721-33-1 KEGG COMPOUND
CHEBI:100241 Drug_Central:659 DrugCentral
CHEBI:100241 PMID:10397494 ChEMBL

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Might be nice to add ORDER BY here.

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Ok