ROBOT Report - ro

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Types of errors

LevelNumber of errors
INFO256
WARN148

Error breakdown

RuleNumber of errors
lowercase_definition256
missing_definition114
annotation_whitespace22
duplicate_exact_synonym8
missing_obsolete_label2
missing_subset_declaration2

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Row Level Rule Name Subject Property Value
0 WARN annotation_whitespace RO:0002101 IAO:0000115 relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @en
1 WARN annotation_whitespace RO:0002103 IAO:0000115 Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. @en
2 WARN annotation_whitespace RO:0002108 IAO:0000424 BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
3 WARN annotation_whitespace RO:0002110 IAO:0000115 Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. @en
4 WARN annotation_whitespace RO:0002115 IAO:0000115 Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
5 WARN annotation_whitespace RO:0002120 IAO:0000115 Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. @en
6 WARN annotation_whitespace RO:0002121 IAO:0000115 Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. @en
7 WARN annotation_whitespace RO:0002132 IAO:0000426 (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and (\"neuron projection bundle ; CARO_0001001\" ?x) (\"neuron projection ; GO0043005\" ?y) (\"neuron projection segment ; CARO_0001502\" ?nps) (\"neuron projection bundle segment ; CARO_0001500\" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
8 WARN annotation_whitespace RO:0002161 IAO:0000425 Class: ?X DisjointWith: RO_0002162 some ?Y
9 WARN annotation_whitespace RO:0002163 IAO:0000116 There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. @en
10 WARN annotation_whitespace RO:0002215 IAO:0000115 A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
11 WARN annotation_whitespace RO:0002256 IAO:0000119 Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
12 WARN annotation_whitespace RO:0002299 IAO:0000112 an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
13 WARN annotation_whitespace RO:0002326 IAO:0000232 In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
14 WARN annotation_whitespace RO:0002341 IAO:0000115 Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
15 WARN annotation_whitespace RO:0002356 IAO:0000115 The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
16 WARN annotation_whitespace RO:0002402 IAO:0000115 p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
17 WARN annotation_whitespace RO:0002504 IAO:0000116 This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
18 WARN annotation_whitespace RO:0002514 IAO:0000115 A relation that holds between two entities that have the property of being sequences or having sequences.
19 WARN annotation_whitespace RO:0002535 IAO:0000232 This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
20 WARN annotation_whitespace RO:HOM0000036 oboInOwl:hasExactSynonym many:many homology
21 WARN annotation_whitespace http://purl.obolibrary.org/obo/ro/ro-base.owl foaf:homepage https://github.com/oborel/obo-relations/^^http://www.w3.org/2001/XMLSchema#anyURI
22 WARN duplicate_exact_synonym RO:0002599 IAO:0000118 treats
23 WARN duplicate_exact_synonym RO:0002606 IAO:0000118 treats
24 WARN duplicate_exact_synonym RO:0002224 IAO:0000118 started by
25 WARN duplicate_exact_synonym RO:0002516 IAO:0000118 started by
26 WARN duplicate_exact_synonym RO:0002409 IAO:0000118 indirectly inhibits
27 WARN duplicate_exact_synonym RO:0011016 IAO:0000118 indirectly inhibits
28 WARN duplicate_exact_synonym RO:0002407 IAO:0000118 indirectly activates
29 WARN duplicate_exact_synonym RO:0011013 IAO:0000118 indirectly activates
30 WARN missing_definition RO:0002001 IAO:0000115
31 WARN missing_definition RO:0002005 IAO:0000115
32 WARN missing_definition RO:0002006 IAO:0000115
33 WARN missing_definition RO:0002016 IAO:0000115
34 WARN missing_definition RO:0002017 IAO:0000115
35 WARN missing_definition RO:0002022 IAO:0000115
36 WARN missing_definition RO:0002081 IAO:0000115
37 WARN missing_definition RO:0002083 IAO:0000115
38 WARN missing_definition RO:0002084 IAO:0000115
39 WARN missing_definition RO:0002085 IAO:0000115
40 WARN missing_definition RO:0002086 IAO:0000115
41 WARN missing_definition RO:0002087 IAO:0000115
42 WARN missing_definition RO:0002088 IAO:0000115
43 WARN missing_definition RO:0002089 IAO:0000115
44 WARN missing_definition RO:0002090 IAO:0000115
45 WARN missing_definition RO:0002091 IAO:0000115
46 WARN missing_definition RO:0002092 IAO:0000115
47 WARN missing_definition RO:0002093 IAO:0000115
48 WARN missing_definition RO:0002111 IAO:0000115
49 WARN missing_definition RO:0002159 IAO:0000115
50 WARN missing_definition RO:0002222 IAO:0000115
51 WARN missing_definition RO:0002259 IAO:0000115
52 WARN missing_definition RO:0002287 IAO:0000115
53 WARN missing_definition RO:0002297 IAO:0000115
54 WARN missing_definition RO:0002300 IAO:0000115
55 WARN missing_definition RO:0002301 IAO:0000115
56 WARN missing_definition RO:0002312 IAO:0000115
57 WARN missing_definition RO:0002322 IAO:0000115
58 WARN missing_definition RO:0002326 IAO:0000115
59 WARN missing_definition RO:0002343 IAO:0000115
60 WARN missing_definition RO:0002344 IAO:0000115
61 WARN missing_definition RO:0002354 IAO:0000115
62 WARN missing_definition RO:0002360 IAO:0000115
63 WARN missing_definition RO:0002405 IAO:0000115
64 WARN missing_definition RO:0002423 IAO:0000115
65 WARN missing_definition RO:0002424 IAO:0000115
66 WARN missing_definition RO:0002425 IAO:0000115
67 WARN missing_definition RO:0002426 IAO:0000115
68 WARN missing_definition RO:0002435 IAO:0000115
69 WARN missing_definition RO:0002447 IAO:0000115
70 WARN missing_definition RO:0002453 IAO:0000115
71 WARN missing_definition RO:0002455 IAO:0000115
72 WARN missing_definition RO:0002456 IAO:0000115
73 WARN missing_definition RO:0002459 IAO:0000115
74 WARN missing_definition RO:0002460 IAO:0000115
75 WARN missing_definition RO:0002461 IAO:0000115
76 WARN missing_definition RO:0002462 IAO:0000115
77 WARN missing_definition RO:0002463 IAO:0000115
78 WARN missing_definition RO:0002464 IAO:0000115
79 WARN missing_definition RO:0002465 IAO:0000115
80 WARN missing_definition RO:0002466 IAO:0000115
81 WARN missing_definition RO:0002467 IAO:0000115
82 WARN missing_definition RO:0002468 IAO:0000115
83 WARN missing_definition RO:0002481 IAO:0000115
84 WARN missing_definition RO:0002482 IAO:0000115
85 WARN missing_definition RO:0002483 IAO:0000115
86 WARN missing_definition RO:0002485 IAO:0000115
87 WARN missing_definition RO:0002486 IAO:0000115
88 WARN missing_definition RO:0002487 IAO:0000115
89 WARN missing_definition RO:0002502 IAO:0000115
90 WARN missing_definition RO:0002506 IAO:0000115
91 WARN missing_definition RO:0002535 IAO:0000115
92 WARN missing_definition RO:0002536 IAO:0000115
93 WARN missing_definition RO:0002537 IAO:0000115
94 WARN missing_definition RO:0002538 IAO:0000115
95 WARN missing_definition RO:0002549 IAO:0000115
96 WARN missing_definition RO:0002550 IAO:0000115
97 WARN missing_definition RO:0002555 IAO:0000115
98 WARN missing_definition RO:0002559 IAO:0000115
99 WARN missing_definition RO:0002563 IAO:0000115
100 WARN missing_definition RO:0002564 IAO:0000115
101 WARN missing_definition RO:0002574 IAO:0000115
102 WARN missing_definition RO:0002580 IAO:0000115
103 WARN missing_definition RO:0002585 IAO:0000115
104 WARN missing_definition RO:0002587 IAO:0000115
105 WARN missing_definition RO:0002588 IAO:0000115
106 WARN missing_definition RO:0002590 IAO:0000115
107 WARN missing_definition RO:0002591 IAO:0000115
108 WARN missing_definition RO:0002611 IAO:0000115
109 WARN missing_definition RO:0002616 IAO:0000115
110 WARN missing_definition RO:0002618 IAO:0000115
111 WARN missing_definition RO:0002619 IAO:0000115
112 WARN missing_definition RO:0002622 IAO:0000115
113 WARN missing_definition RO:0002623 IAO:0000115
114 WARN missing_definition RO:0002624 IAO:0000115
115 WARN missing_definition RO:0002625 IAO:0000115
116 WARN missing_definition RO:0002626 IAO:0000115
117 WARN missing_definition RO:0002627 IAO:0000115
118 WARN missing_definition RO:0002634 IAO:0000115
119 WARN missing_definition RO:0002635 IAO:0000115
120 WARN missing_definition RO:0004000 IAO:0000115
121 WARN missing_definition RO:0004001 IAO:0000115
122 WARN missing_definition RO:0004002 IAO:0000115
123 WARN missing_definition RO:0004003 IAO:0000115
124 WARN missing_definition RO:0004004 IAO:0000115
125 WARN missing_definition RO:0004005 IAO:0000115
126 WARN missing_definition RO:0004006 IAO:0000115
127 WARN missing_definition RO:0004010 IAO:0000115
128 WARN missing_definition RO:0004017 IAO:0000115
129 WARN missing_definition RO:0004018 IAO:0000115
130 WARN missing_definition RO:0004019 IAO:0000115
131 WARN missing_definition RO:0004023 IAO:0000115
132 WARN missing_definition RO:0004025 IAO:0000115
133 WARN missing_definition RO:0004032 IAO:0000115
134 WARN missing_definition RO:0004033 IAO:0000115
135 WARN missing_definition RO:0004046 IAO:0000115
136 WARN missing_definition RO:0004047 IAO:0000115
137 WARN missing_definition RO:0004049 IAO:0000115
138 WARN missing_definition RO:0004050 IAO:0000115
139 WARN missing_definition RO:0012008 IAO:0000115
140 WARN missing_definition RO:0015002 IAO:0000115
141 WARN missing_definition RO:0015010 IAO:0000115
142 WARN missing_definition RO:0016001 IAO:0000115
143 WARN missing_definition RO:0018030 IAO:0000115
144 WARN missing_obsolete_label RO:0004096 rdfs:label DEPRECATED inheres in@en
145 WARN missing_obsolete_label RO:0004097 rdfs:label DEPRECATED bearer of@en
146 WARN missing_subset_declaration RO:0002259 rdfs:subPropertyOf
147 WARN missing_subset_declaration obo:ro/subsets#ro-eco rdfs:subPropertyOf
148 INFO lowercase_definition RO:0000052 IAO:0000115 a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.@en
149 INFO lowercase_definition RO:0000056 IAO:0000115 a relation between a continuant and a process, in which the continuant is somehow involved in the process@en
150 INFO lowercase_definition RO:0000057 IAO:0000115 a relation between a process and a continuant, in which the continuant is somehow involved in the process@en
151 INFO lowercase_definition RO:0000079 IAO:0000115 a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence@en
152 INFO lowercase_definition RO:0000080 IAO:0000115 a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence@en
153 INFO lowercase_definition RO:0000081 IAO:0000115 a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence@en
154 INFO lowercase_definition RO:0000085 IAO:0000115 a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence@en
155 INFO lowercase_definition RO:0000086 IAO:0000115 a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence@en
156 INFO lowercase_definition RO:0000087 IAO:0000115 a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence@en
157 INFO lowercase_definition RO:0000091 IAO:0000115 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence@en
158 INFO lowercase_definition RO:0000092 IAO:0000115 inverse of has disposition
159 INFO lowercase_definition RO:0001000 IAO:0000115 a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity@en
160 INFO lowercase_definition RO:0001001 IAO:0000115 a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity@en
161 INFO lowercase_definition RO:0001015 IAO:0000115 a relation between two independent continuants, the location and the target, in which the target is entirely within the location@en
162 INFO lowercase_definition RO:0001025 IAO:0000115 a relation between two independent continuants, the target and the location, in which the target is entirely within the location@en
163 INFO lowercase_definition RO:0001901 IAO:0000115 ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
164 INFO lowercase_definition RO:0001902 IAO:0000115 ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)
165 INFO lowercase_definition RO:0002000 IAO:0000115 a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity@en
166 INFO lowercase_definition RO:0002002 IAO:0000115 a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity@en
167 INFO lowercase_definition RO:0002010 IAO:0000115 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
168 INFO lowercase_definition RO:0002018 IAO:0000115 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
169 INFO lowercase_definition RO:0002082 IAO:0000115 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.
170 INFO lowercase_definition RO:0002101 IAO:0000115 relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @en
171 INFO lowercase_definition RO:0002120 IAO:0000115 Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. @en
172 INFO lowercase_definition RO:0002131 IAO:0000115 x overlaps y if and only if there exists some z such that x has part z and z part of y
173 INFO lowercase_definition RO:0002151 IAO:0000115 x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
174 INFO lowercase_definition RO:0002156 IAO:0000115 d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
175 INFO lowercase_definition RO:0002157 IAO:0000115 inverse of derived by descent from
176 INFO lowercase_definition RO:0002158 IAO:0000115 two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
177 INFO lowercase_definition RO:0002160 IAO:0000115 x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
178 INFO lowercase_definition RO:0002161 IAO:0000115 x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
179 INFO lowercase_definition RO:0002162 IAO:0000115 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
180 INFO lowercase_definition RO:0002170 IAO:0000115 a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
181 INFO lowercase_definition RO:0002176 IAO:0000115 c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
182 INFO lowercase_definition RO:0002177 IAO:0000115 a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
183 INFO lowercase_definition RO:0002180 IAO:0000115 w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
184 INFO lowercase_definition RO:0002201 IAO:0000115 inverse of has phenotype
185 INFO lowercase_definition RO:0002202 IAO:0000115 x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
186 INFO lowercase_definition RO:0002203 IAO:0000115 inverse of develops from
187 INFO lowercase_definition RO:0002204 IAO:0000115 definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"
188 INFO lowercase_definition RO:0002205 IAO:0000115 x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
189 INFO lowercase_definition RO:0002206 IAO:0000115 x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
190 INFO lowercase_definition RO:0002209 IAO:0000115 inverse of parasitoid of
191 INFO lowercase_definition RO:0002210 IAO:0000115 inverse of directly develops from
192 INFO lowercase_definition RO:0002211 IAO:0000115 p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
193 INFO lowercase_definition RO:0002212 IAO:0000115 p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
194 INFO lowercase_definition RO:0002213 IAO:0000115 p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
195 INFO lowercase_definition RO:0002214 IAO:0000115 x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation.
196 INFO lowercase_definition RO:0002216 IAO:0000115 c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
197 INFO lowercase_definition RO:0002219 IAO:0000115 x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
198 INFO lowercase_definition RO:0002220 IAO:0000115 x adjacent to y if and only if x and y share a boundary.
199 INFO lowercase_definition RO:0002221 IAO:0000115 inverse of surrounded by