Model changes to capture and consolidate human disease data
A new tag ‘Disease_info’ proposed to consolidate disease-related data in WormBase:
?Gene DB_info Database ?Database ?Database_field Text Disease_info Experimental_model_for_human ?DO_term XREF Gene_by_biology #Evidence Potential_model_for_human ?DO_term XREF Gene_by_orthology #Evidence Human_disease_relevance ?Text #Evidence //moved from ‘structured description’ tag.
Model for Disease Ontology Term:
?DO_term Name ?Text Status UNIQUE Valid Obsolete Alternate_id ?Text Definition ?Text Comment Text Synonymn ?Text Scope_modifier UNIQUE Broad Exact Narrow Related Relationship is_a ?DO_term DB_info Database ?Database ?Database_field Text //to reference OMIM Replaced_by ?DO_term Subset Text Created_by Text Creation_date Text Attribute_of Gene_by_biology ?Gene XREF DO_term Gene_by_orthology ?Gene XREF DO_term Phenotype ?Phenotype XREF DO_term WBProcess ?WBProcess XREF DO_term Reference ?Paper XREF DO_term Index Ancestor ?DO_term //Consider transitivity, needed for web display? Descendent ?DO_term //Consider transitivity, needed for web display? Version UNIQUE Text //revision number
Paul D's suggestions/corrections: For the 'Disease_info' tag under ?Gene:
- Add ?Species tag instead of 'Experimental_model_for_human' type tags, to indicate species information.
For ?DO_term model:
- Drop 'Created_by' and 'Creation_date', not useful information to import, check original source of information if needed.
- For the 'subset' tag, follow standard procedure across models:
?DO_term Type GOLD gram-negative_bacterial_infectious_disease gram-positive_bacterial_infectious_disease sexually_transmitted_infectious_disease tick-borne_infectious_disease zoonotic_infectious_disease
Ideally this would have been UNIQUE but there are 178 DO_terms with multiple subset lines populated.
Or is there something better that maintains flexibility but controls the vocabulary better that Text
- This tag structure isn't workable as there isn't a general DO_term tag in the ?Gene model and it's a 2:1.
?DO_term Attribute_of Gene_by_biology ?Gene XREF DO_term Gene_by_orthology ?Gene XREF DO_term
- This is also not a permitted tag combination, you aren't allowed to build a branch off a Text/?Text tag, this might be a bug in the acedb code so I have raised a ticket with the acedb dev team, but as of now it's a show stopper, could you re-think this section.
?DO_term Synonymn ?Text Scope_modifier UNIQUE Broad Exact Narrow Related
- Relationships--Could we also modify the Relationship section as the proposed tag names are new and relationships are used in multiple other classes, could you copy one of the other models as I just created some test data and had the relationship reversed because of the tag names and I wasn't being careful. We should try and re-use common tag structures, that was if there are enough of them we can move them into a Hash to simplify the models file.
?Anatomy_term Lineage Parent_term UNIQUE ?Anatomy_term XREF Daughter_term Daughter_term ?Anatomy_term XREF Parent_term ?SO_term Parent Is_a ?SO_term XREF Is Part_of ?SO_term XREF Part Derived_from ?SO_term XREF Derives Member_of ?SO_term XREF Member Child Is ?SO_term XREF Is_a Part ?SO_term XREF Part_of Derives ?SO_term XREF Derived_from Member ?SO_term XREF Member_of ?Cell Lineage Parent UNIQUE ?Cell XREF Daughter Daughter ?Cell XREF Parent ?GO_term Child Instance ?GO_term XREF Instance_of Component ?GO_term XREF Component_of Parent Instance_of ?GO_term XREF Instance Component_of ?GO_term XREF Component
- Index and Relationship--Are these not storing the same data?