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Ubergraph IRI to curie conversions #342
Description
While parsing Ubergraph we use this package to convert URIs from Ubergraph to curies, but there are a significant number of failures. We should double check that we're not losing stuff we'd like for that reason. Notably, it looks like we're losing emapa#part_of and some ncbigenes.
Currently
Nodes: 3975857 successfully converted, 178738 failures.
Edges: 601 successfully converted, 49 failures.
Node conversion failure examples: ['https://bar.utoronto.ca/thalemine/portal.do?externalids=AT5G62890', 'http://identifiers.org/ncbigene/379028', 'http://identifiers.org/ncbigene/100420113', 'http://identifiers.org/ncbigene/100132863', 'http://identifiers.org/ncbigene/104472714', 'http://identifiers.org/ncbigene/729392', 'http://identifiers.org/ncbigene/100359397', 'http://flybase.org/reports/FBgn0002945', 'http://www.informatics.jax.org/marker/MGI:1345171', 'http://www.informatics.jax.org/marker/MGI:1346869']
Edge conversion failure examples: ['http://purl.obolibrary.org/obo/mondo#disease_responds_to', 'http://purl.obolibrary.org/obo/so#overlaps', 'http://purl.obolibrary.org/obo/so#derives_from', 'http://purl.obolibrary.org/obo/chebi#has_functional_parent', 'http://purl.obolibrary.org/obo/emapa#part_of', 'http://purl.obolibrary.org/obo/pr#has_gene_template', 'http://purl.obolibrary.org/obo/chebi#is_substituent_group_from', 'http://purl.obolibrary.org/obo/emapa#ends_at', 'http://purl.obolibrary.org/obo/so#variant_of', 'http://purl.obolibrary.org/obo/bspo#parallel_to']
Activity
hina-shah commentedon Oct 14, 2025
Running the parsing on curies package version 0.10.23 returns:
Nodes: 3779212 successfully converted, 104084 failures. (~2.75%)
Edges: 542 successfully converted, 46 failures. (~8.48%)
Node conversion failure examples: ['http://www.wormbase.org/species/c_elegans/gene/WBGene00003680', 'http://www.ecogene.org/gene/EG11222', 'http://www.yeastgenome.org/locus/S000004843', 'http://zfin.org/action/marker/view/ZDB-GENE-000403-1', 'http://www.ncbi.nlm.nih.gov/gene/395786', 'http://flybase.org/reports/FBgn0026597', 'http://www.informatics.jax.org/marker/MGI:1096327', 'http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=620859', 'http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=903', 'http://www.informatics.jax.org/marker/MGI:1858259']
Edge conversion failure examples: ['http://purl.obolibrary.org/obo/chebi#has_functional_parent', 'http://purl.obolibrary.org/obo/pr#lacks_part', 'http://purl.obolibrary.org/obo/pr#has_gene_template', 'http://purl.obolibrary.org/obo/chebi#is_conjugate_base_of', 'http://purl.obolibrary.org/obo/mondo#predisposes_towards', 'http://purl.obolibrary.org/obo/emapa#part_of', 'http://purl.obolibrary.org/obo/emapa#starts_at', 'http://purl.obolibrary.org/obo/emapa#ends_at', 'http://purl.obolibrary.org/obo/mondo#disease_has_major_feature', 'http://purl.obolibrary.org/obo/chebi#is_conjugate_acid_of']
Full list of failures is attached.
edge_mapping_failures.txt
node_mapping_failures.txt