ROBOT Report - iao

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Row Level Rule Name Subject Property Value
0 WARN annotation_whitespace IAO:0000009 IAO:0000232 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
1 WARN annotation_whitespace IAO:0000115 IAO:0000116 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. @en
2 WARN annotation_whitespace IAO:0000424 IAO:0000112 ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 \" some ( and some ?Y)\" @en
3 WARN annotation_whitespace IAO:0000425 IAO:0000112 ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to \"DisjointClasses: ( some ?X) ( some ?Y)\" @en
4 WARN annotation_whitespace IAO:0000575 IAO:0000112 Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
5 WARN annotation_whitespace IAO:0000579 IAO:0000112 PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. @en
6 WARN annotation_whitespace IAO:0000580 IAO:0000112 Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
7 WARN annotation_whitespace IAO:0000597 IAO:0000112 Datatype: idrange:1 Annotations: 'has ID range allocated to': \"Chris Mungall\" EquivalentTo: xsd:integer[> 2151 , <= 2300] @en
8 WARN annotation_whitespace IAO:0000617 IAO:0000112 SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (] @en
9 WARN annotation_whitespace IAO:0000640 IAO:0000112 Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. ( Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). @en
10 WARN duplicate_exact_synonym IAO:0000609 IAO:0000118
11 WARN duplicate_exact_synonym IAO:0000615 IAO:0000118
12 WARN missing_definition IAO:0000004 IAO:0000115
13 WARN missing_definition IAO:0000034 IAO:0000115
14 WARN missing_definition IAO:0000039 IAO:0000115
15 WARN missing_definition IAO:0000057 IAO:0000115
16 WARN missing_definition IAO:0000114 IAO:0000115
17 WARN missing_definition IAO:0000404 IAO:0000115
18 WARN missing_definition IAO:0000405 IAO:0000115
19 WARN missing_definition IAO:0000406 IAO:0000115
20 WARN missing_definition IAO:0000407 IAO:0000115
21 WARN missing_definition IAO:0000426 IAO:0000115
22 WARN missing_definition IAO:0000429 IAO:0000115
23 WARN missing_definition IAO:0000582 IAO:0000115
24 WARN missing_definition IAO:8000000 IAO:0000115
25 WARN missing_definition IAO:8000016 IAO:0000115
26 WARN missing_definition IAO:8000017 IAO:0000115
27 WARN missing_definition IAO:8000019 IAO:0000115
28 WARN missing_definition IAO:8000020 IAO:0000115
29 INFO lowercase_definition IAO:0000024 IAO:0000115 a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
30 INFO lowercase_definition IAO:0000135 IAO:0000115 c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
31 INFO lowercase_definition IAO:0000221 IAO:0000115 m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q@en
32 INFO lowercase_definition IAO:0000235 IAO:0000115 inverse of the relation 'denotes'@en
33 INFO lowercase_definition IAO:0000413 IAO:0000115 relates a process to a time-measurement-datum that represents the duration of the process@en
34 INFO lowercase_definition IAO:0000417 IAO:0000115 inverse of the relation of is quality measurement of@en
35 INFO lowercase_definition IAO:0000419 IAO:0000115 inverse of the relation of is quality specification of@en
36 INFO lowercase_definition IAO:0000576 IAO:0000115 a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
37 INFO lowercase_definition IAO:0000581 IAO:0000115 relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken@en
38 INFO lowercase_definition IAO:0000583 IAO:0000115 relates a time stamped measurement datum to the measurement datum that was measured@en
39 INFO lowercase_definition IAO:0000604 IAO:0000115 relates a class of CRID to the date after which further instances should not be made, according to the central authority