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INCATools / ubergraph

Integrated OBO ontology store
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eliminate OBO hash IRIs #102

Open balhoff opened 2 years ago

balhoff commented 2 years ago

A number of ontologies have properties with non-standard OBO identifier structures. These reduce integration in Ubergraph. Ideally all these would be either added to RO or given identifiers in their ontology namespaces. Some examples:

http://purl.obolibrary.org/obo/bspo#parallel_to
http://purl.obolibrary.org/obo/chebi#has_functional_parent
http://purl.obolibrary.org/obo/chebi#has_parent_hydride
http://purl.obolibrary.org/obo/chebi#is_conjugate_acid_of
http://purl.obolibrary.org/obo/chebi#is_conjugate_base_of
http://purl.obolibrary.org/obo/chebi#is_enantiomer_of
http://purl.obolibrary.org/obo/chebi#is_substituent_group_from
http://purl.obolibrary.org/obo/cl#has_completed
http://purl.obolibrary.org/obo/cl#has_not_completed
http://purl.obolibrary.org/obo/cl#lacks_part
http://purl.obolibrary.org/obo/cl#lacks_plasma_membrane_part
http://purl.obolibrary.org/obo/emapa#develops_from
http://purl.obolibrary.org/obo/emapa#ends_at
http://purl.obolibrary.org/obo/emapa#part_of
http://purl.obolibrary.org/obo/emapa#starts_at
http://purl.obolibrary.org/obo/envo#has_increased_levels_of
http://purl.obolibrary.org/obo/excluded_subClassOf
http://purl.obolibrary.org/obo/fbcv#conditionality
http://purl.obolibrary.org/obo/fypo#has_output
http://purl.obolibrary.org/obo/fypo#output_of
http://purl.obolibrary.org/obo/ma#part_of
http://purl.obolibrary.org/obo/mi#part_of
http://purl.obolibrary.org/obo/mondo#disease_causes_feature
http://purl.obolibrary.org/obo/mondo#disease_has_basis_in_accumulation_of
http://purl.obolibrary.org/obo/mondo#disease_has_basis_in_development_of
http://purl.obolibrary.org/obo/mondo#disease_has_major_feature
http://purl.obolibrary.org/obo/mondo#disease_responds_to
http://purl.obolibrary.org/obo/mondo#disease_shares_features_of
http://purl.obolibrary.org/obo/mondo#disease_triggers
http://purl.obolibrary.org/obo/mondo#has_onset
http://purl.obolibrary.org/obo/mondo#has_onset_before
http://purl.obolibrary.org/obo/mondo#has_onset_during_or_after
http://purl.obolibrary.org/obo/mondo#part_of_progression_of_disease
http://purl.obolibrary.org/obo/mondo#predisposes_towards
http://purl.obolibrary.org/obo/peco#part_of
http://purl.obolibrary.org/obo/po#derives_by_manipulation_from
http://purl.obolibrary.org/obo/pr#confers_resistance_to
http://purl.obolibrary.org/obo/pr#has_gene_template
http://purl.obolibrary.org/obo/pr#lacks_part
http://purl.obolibrary.org/obo/pr#non-covalently_bound_to
http://purl.obolibrary.org/obo/so#adjacent_to
http://purl.obolibrary.org/obo/so#contains
http://purl.obolibrary.org/obo/so#derives_from
http://purl.obolibrary.org/obo/so#guided_by
http://purl.obolibrary.org/obo/so#has_origin
http://purl.obolibrary.org/obo/so#has_part
http://purl.obolibrary.org/obo/so#has_quality
http://purl.obolibrary.org/obo/so#member_of
http://purl.obolibrary.org/obo/so#non_functional_homolog_of
http://purl.obolibrary.org/obo/so#overlaps
http://purl.obolibrary.org/obo/so#part_of
http://purl.obolibrary.org/obo/so#transcribed_from
http://purl.obolibrary.org/obo/so#transcribed_to
http://purl.obolibrary.org/obo/so#variant_of
cthoyt commented 2 years ago

Even worse, there are tons of the same relations that are being duplicated with these crazy hash relations. I've been curating a list of ways to auto-upgrade these to the appropriate RO terms when possible (and making a normalized namespace DeBiO for everything else) here: https://github.com/biopragmatics/bioontologies/blob/main/src/bioontologies/upgrade/data.tsv

matentzn commented 2 years ago

Most of these are accidents but not all. Maybe make a google spreadsheet and we map these to RO where an RO mapping exist, then make issues at the relevant ontologies to change their IRIs.

balhoff commented 2 years ago

Linked issues:

anitacaron commented 2 years ago

One more linked issue from CL.

anitacaron commented 1 year ago

General ticket in Uberon: