INCATools / INCATools/ubergraph

eliminate OBO hash IRIs

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Description

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
```

Contributor guide

No contributing guide indexed for this repository

Research direction

No files, tests, or entry points are named. Start by identifying how Ubergraph ingests and normalizes the listed OBO IRIs, then establish namespace replacements for each case and verify that the affected identifiers no longer use non-standard hash structures.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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