metaproteomics update #146
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WalkthroughThis pull request adds a substantial number of new ontology terms to the Changes
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pride_cv.obo (1)
4003-4009: Initial addition of 'human gut' term looks good overall.
| id: PRIDE:0000677 | ||
| name: gastrointestinal tract disorder | ||
| def: "History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280" [PRIDE:PRIDE] | ||
| is_a: MONDO:0000001 ! Disease | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000678 | ||
| name: liver disorder | ||
| def: "History of liver disorders; can include multiple disorders. MIXS:0000282" [PRIDE:PRIDE] | ||
| is_a: MONDO:0000001 ! Disease | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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Avoid using 'human gut' as a parent for disease terms.
The new terms gastrointestinal tract disorder (lines 4031–4036) and liver disorder (lines 4040–4044) both inherit from MONDO:0000001 ! Disease and PRIDE:0000674 ! Human gut. This dual inheritance is semantically inconsistent, because a disease entity should not also be classified as an anatomical entity. Consider modeling these relationships with alternative properties (e.g., occurs_in or part_of), rather than is_a.
| def: "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888" [PRIDE:PRIDE] | ||
| is_a: NCIT:C12219 ! Anatomic Structure, System, or Substance | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000687 | ||
| name: host total mass | ||
| def: "Total mass of the host at collection, the unit depends on host. MIXS:0000263" [PRIDE:PRIDE] | ||
| is_a: OBA:2045413 ! anatomical entity mass | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000688 | ||
| name: host height | ||
| def: "The height of subject. MIXS:0000264" [PRIDE:PRIDE] | ||
| synonym: "body height" EXACT [] | ||
| is_a: NCIT:C25347 ! Height | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000689 | ||
| name: host diet | ||
| def: "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. MIXS:0000869" [PRIDE:PRIDE] | ||
| is_a: EFO:0002755 ! Diet | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000690 | ||
| name: host last meal | ||
| def: "Content of last meal and time since feeding; can include multiple values. MIXS:0000870" [PRIDE:PRIDE] | ||
| is_a: NCIT:C80248 ! Meal | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000691 | ||
| name: host family relationship | ||
| def: "Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872" [PRIDE:PRIDE] | ||
| synonym: "family relationship" EXACT [] | ||
| is_a: BFO:0000016 ! disposition | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000692 | ||
| name: host genotype | ||
| def: "Observed genotype MIXS:0000365" [PRIDE:PRIDE] | ||
| is_a: EFO:0004554 ! genomic measurement | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000693 | ||
| name: host phenotype | ||
| def: "Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274" [PRIDE:PRIDE] | ||
| is_a: BFO:0000019 ! quality | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000694 | ||
| name: host body temperature | ||
| def: "Core body temperature of the host when sample was collected. MIXS:0000874" [PRIDE:PRIDE] | ||
| is_a: NCIT:C25206 ! Temperature | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000695 | ||
| name: host body-mass index | ||
| def: "Body mass index, calculated as weight/(height)squared. MIXS:0000317" [PRIDE:PRIDE] | ||
| is_a: EFO:0004324 ! body weights and measurements | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000696 | ||
| name: ethnicity | ||
| def: "A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. MIXS:0000895" [PRIDE:PRIDE] | ||
| is_a: BFO:0000019 ! quality | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000697 | ||
| name: host occupation | ||
| def: "Most frequent job performed by subject. MIXS:0000896" [PRIDE:PRIDE] | ||
| is_a: NCIT:C19160 ! Occupation or Discipline | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000698 | ||
| name: medical history performed | ||
| def: "Whether full medical history was collected. MIXS:0000897" [PRIDE:PRIDE] | ||
| is_a: NCIT:C16205 ! Healthcare activity | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000699 | ||
| name: host pulse | ||
| def: "Resting pulse, measured as beats per minutes. MIXS:0000333" [PRIDE:PRIDE] | ||
| is_a: PRIDE:0000674 ! Human gut | ||
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| [Term] | ||
| id: PRIDE:0000700 | ||
| name: perturbation | ||
| def: "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types. MIXS:0000754" [PRIDE:PRIDE] |
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Re-examine “is_a” relationships for data fields and descriptors.
Many newly introduced terms (e.g., sample name, project name, special diet, host subject id, host age, host diet, etc.) are declared with is_a: PRIDE:0000674 ! human gut, is_a: PRIDE:0000828 ! Soil, or is_a: PRIDE:0000829 ! Water. Data fields, disease statuses, or descriptors are not true subtypes of these anatomical or environmental entities. Instead of is_a, consider using relationships better suited for describing context or usage, such as applies_to_environment, collected_in, used_for, or part_of.
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Actionable comments posted: 1
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🔇 Additional comments (5)
pride_cv.obo (5)
4010-4019: Re-examine the 'is_a' relationships for data fields.Using "human gut," "soil," or "water" as parents for a data field (sample name) is semantically incorrect. Per the previous reviewer’s feedback, consider relationships like collected_in, applicable_environment, or part_of, instead of
is_a.
4020-4029: Re-examine the 'is_a' relationships for data fields.Using "human gut," "soil," or "water" as parents for a data field (project name) is semantically incorrect. Consider modeling these relationships with a property more fitting than
is_a.
4030-4036: Avoid using 'human gut' as a parent for disease terms.Diseases (e.g., gastrointestinal tract disorder) should not inherit from an anatomical entity. Consider alternative properties such as occurs_in or associated_with, rather than
is_a.
4038-4044: Avoid using 'human gut' as a parent for disease terms.Diseases (e.g., liver disorder) should not be declared as subtypes of an anatomical or environmental entity. Use a more appropriate relationship than
is_a.
4121-4122: Correct spelling of “Mediterranean.”Please fix the typographical error in the definition.
- def: "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include..." + def: "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include..."
Metaproteomics with changes
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