unify annotations

[shawntanzk]

Add documentations on how each of the ontologies handle things like created by and xrefs (I've been noticing that there each one handles it differently and it's sometimes not consistent within ontology)

Related to: pato-ontology/pato#278

[shawntanzk]

Plan:

• @anitacaron will generate a report on what the most used annotations are
• Write documentation of prevailing annotation so that people will use it (should also be announced in meetings/slack/etc.)
• Create automatic checks that force the use of those annotations

[anitacaron]

ANNOTATION	UBERON	CL	PATO	RO
http://geneontology.org/formats/oboInOwl#created_by		3
http://purl.obolibrary.org/obo/IAO_0000115	11762	2141	1851
http://purl.obolibrary.org/obo/IAO_0000116	910	1
http://purl.obolibrary.org/obo/IAO_0000231	291		84
http://purl.obolibrary.org/obo/IAO_0000232	240			69
http://purl.obolibrary.org/obo/IAO_0000412		2
http://purl.obolibrary.org/obo/IAO_0000589			1	22
http://purl.obolibrary.org/obo/IAO_0100001	512	26	90	2
http://purl.obolibrary.org/obo/RO_0002161	272	1
http://purl.obolibrary.org/obo/RO_0002173	4
http://purl.obolibrary.org/obo/RO_0002174	42
http://purl.obolibrary.org/obo/RO_0002175	312	4
http://purl.obolibrary.org/obo/RO_0002423				1
http://purl.obolibrary.org/obo/RO_0002575				6
http://purl.obolibrary.org/obo/RO_0002579				2
http://purl.obolibrary.org/obo/RO_0002604			425
http://purl.obolibrary.org/obo/RO_0004049				7
http://purl.obolibrary.org/obo/RO_0004050				7
http://purl.obolibrary.org/obo/RO_0040042				2
http://purl.obolibrary.org/obo/UBPROP_0000001	1605
http://purl.obolibrary.org/obo/UBPROP_0000002	195
http://purl.obolibrary.org/obo/UBPROP_0000003	623
http://purl.obolibrary.org/obo/UBPROP_0000004	2470
http://purl.obolibrary.org/obo/UBPROP_0000005	23
http://purl.obolibrary.org/obo/UBPROP_0000006	88
http://purl.obolibrary.org/obo/UBPROP_0000007	315
http://purl.obolibrary.org/obo/UBPROP_0000008	815
http://purl.obolibrary.org/obo/UBPROP_0000009	159
http://purl.obolibrary.org/obo/UBPROP_0000010	114
http://purl.obolibrary.org/obo/UBPROP_0000011	157
http://purl.obolibrary.org/obo/UBPROP_0000012	646
http://purl.obolibrary.org/obo/UBPROP_0000013	67
http://purl.obolibrary.org/obo/UBPROP_0000014	14
http://purl.obolibrary.org/obo/UBPROP_0000015	13
http://purl.obolibrary.org/obo/UBPROP_0000103	8
http://purl.obolibrary.org/obo/UBPROP_0000104	24
http://purl.obolibrary.org/obo/UBPROP_0000105	1
http://purl.obolibrary.org/obo/UBPROP_0000106	12
http://purl.obolibrary.org/obo/UBPROP_0000107	19
http://purl.obolibrary.org/obo/UBPROP_0000108	30
http://purl.obolibrary.org/obo/UBPROP_0000111	8
http://purl.obolibrary.org/obo/UBPROP_0000112	11
http://purl.obolibrary.org/obo/UBPROP_0000201	11
http://purl.obolibrary.org/obo/UBPROP_0000202	43
http://purl.obolibrary.org/obo/term_editor	21
http://purl.org/dc/elements/1.1/contributor	299	1	3	7
http://purl.org/dc/elements/1.1/creator	7	93	4	9
http://purl.org/dc/elements/1.1/date	28	24	25
http://purl.org/dc/elements/1.1/description	2			1
http://purl.org/dc/terms/source				2
http://purl.org/spar/cito/citesAsAuthority				41
http://www.geneontology.org/formats/oboInOwl#consider	809	26	3
http://www.geneontology.org/formats/oboInOwl#created_by	3074	873	733	80
http://www.geneontology.org/formats/oboInOwl#creation_date	37	759	630	79
http://www.geneontology.org/formats/oboInOwl#hasAlternativeId	341	74	84
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym	1297	183	12
http://www.geneontology.org/formats/oboInOwl#hasDbXref	49662	1475	53
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym	25684	2013	623
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym	813	35	22
http://www.geneontology.org/formats/oboInOwl#hasOBONamespace	15228	2177	2738
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym	11777	242	257
http://www.geneontology.org/formats/oboInOwl#id	15228	101	2738
http://www.geneontology.org/formats/oboInOwl#inSubset	5827	143	2729	224
http://www.w3.org/2000/01/rdf-schema#comment	993	486	102
http://www.w3.org/2000/01/rdf-schema#label	15229	2542	2738
http://www.w3.org/2000/01/rdf-schema#seeAlso	127	7		92
http://www.w3.org/2004/02/skos/core#closeMatch				3
http://www.w3.org/2002/07/owl#deprecated	1338	130	977
http://xmlns.com/foaf/0.1/depicted_by	1885	1

[matentzn]

This is more than perfect, great work @anitacaron

[shawntanzk]

omg that is such a great table! thanks!

[anitacaron]

ANNOTATION	LABEL	DESCRIPTION
http://purl.obolibrary.org/obo/UBPROP_0000001	external_definition	An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
http://purl.obolibrary.org/obo/UBPROP_0000002	axiom_lost_from_external_ontology	A textual description of an axiom loss in this ontology compared to an external ontology.
http://purl.obolibrary.org/obo/UBPROP_0000003	homology_notes	Notes on the homology status of this class.
http://purl.obolibrary.org/obo/UBPROP_0000005	external_comment	An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
http://purl.obolibrary.org/obo/UBPROP_0000008	taxon_notes	Notes on the how instances of this class vary across species.
http://purl.obolibrary.org/obo/UBPROP_0000009	function_notes	Notes on the evolved function of instances of this class.
http://purl.obolibrary.org/obo/UBPROP_0000010	structure_notes	Notes on the structure, composition or histology of instances of this class.
http://purl.obolibrary.org/obo/UBPROP_0000011	development_notes	Notes on the ontogenic development of instances of this class.
http://purl.obolibrary.org/obo/UBPROP_0000012	external_ontology_notes	Notes on how similar or equivalent classes are represented in other ontologies.
http://purl.obolibrary.org/obo/UBPROP_0000013	terminology_notes	Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
http://purl.obolibrary.org/obo/UBPROP_0000014	actions_notes	Notes on how instances of this class functon biomechanically.
http://purl.obolibrary.org/obo/UBPROP_0000015	location_notes	Notes on the location, position or part-parents of instances of this class.
http://purl.obolibrary.org/obo/UBPROP_0000101	preceding element is	A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates).
http://purl.obolibrary.org/obo/UBPROP_0000102	repeated element number	A property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral condition.
http://purl.obolibrary.org/obo/UBPROP_0000103	pharyngeal arch number	x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
http://purl.obolibrary.org/obo/UBPROP_0000104	ray number	x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray.
http://purl.obolibrary.org/obo/UBPROP_0000105	phalanx number	x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2.
http://purl.obolibrary.org/obo/UBPROP_0000106	rib number	x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, not the adjoining vertebrae.
http://purl.obolibrary.org/obo/UBPROP_0000107	vertebra number	x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas).
http://purl.obolibrary.org/obo/UBPROP_0000108	somite number	x somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite.
http://purl.obolibrary.org/obo/UBPROP_0000109	paired_appendage number	x paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendage.
http://purl.obolibrary.org/obo/UBPROP_0000110	appendage segment number	x appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments).
http://purl.obolibrary.org/obo/UBPROP_0000111	rhombomere number	x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere.
http://purl.obolibrary.org/obo/UBPROP_0000112	tooth number	x tooth_number N if and only if (i) x is a tooth, and (ii) x is ancestrally tooth number N in a series of teeth repeated along an anterior-posterior axis, typically on the lateral side of a structure such as a jaw, with tooth_number 1 being the anteriormost. Note that this count refers to the total number of teeth starting from the first, regardless of the type of tooth. If sub-systems are required for numbering within a series of teeth of the same type, consider a subproperty. For example, in a human, maxillary canine = tooth 3 of upper jaw = canine_tooth 1 of upper jaw.
http://purl.obolibrary.org/obo/UBPROP_0000113	dental formula	Syntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property.

[matentzn]

@anitacaron thats great, I will run this by @cmungall and see whether we want to maintain them all. If so, we will write documentation on when and why to add these.

[cmungall]

This is great, thanks. These are in two categories

1. specialized notes fields (range: text)
2. logical axiom shortcuts (range: typically integer)

For 1 I have no string opinions. Keep UBPROP, move to UBERON namespace, move specific terms to OMO, use generic OMO terms with some kind of qualifier [e.g. "note about topic X" OMO pattern]. You all decide!

2 is more interesting. These axioms aren't doing much work at the moment but I wager they will be crucial for comparative use cases. We know that representing these more directly in OWL doesn't work (https://douroucouli.wordpress.com/2021/03/24/avoid-mixing-parthood-with-cardinality-constraints/). They are certainly not appropriate for OMO. I would favor keeping them in the ontology for now. I don't have strong opinions on whether we keep UBPROP for these, move to UBERON namespace, make RO shortcuts, put these in PATO, or have an entirely different approach for this kind of thing (e.g. lightweight w3id URIs).

[shawntanzk]

From the above, we suggest removing the following as they are not really being used:
http://purl.obolibrary.org/obo/IAO_0000412
http://purl.obolibrary.org/obo/term_editor (should be moved to dc:creator or dc:contributor)
http://purl.org/dc/elements/1.1/description (will be moved to either rdfs:comment or IAO_0000115)

The following need to be checked by @matentzn and we will remove if they are not useful:

• http://purl.obolibrary.org/obo/IAO_0000589 (issue)
• http://purl.obolibrary.org/obo/RO_0002579 (do not delete)
• http://purl.obolibrary.org/obo/RO_0002575 (do not delete)
• http://purl.obolibrary.org/obo/RO_0002423 (do not delete)

@shawntanzk will check what the following are:
http://purl.org/dc/terms/source
http://purl.org/spar/cito/citesAsAuthority
where in UBERON http://purl.obolibrary.org/obo/RO_0002173 is used and what for

Tickets will be made for other things

[cmungall]

http://purl.obolibrary.org/obo/RO_0002173 (ambiguous for taxon) is logically silent but says "it's quite likely we would want to place a taxon constrain here but can't for a number of reasons". I suppose these could be replaced by issues. But I like making this transparent.