| 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 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"
@en |
| 3 |
WARN |
annotation_whitespace |
IAO:0000425 |
IAO:0000112 |
ObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 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 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] @en |
| 9 |
WARN |
annotation_whitespace |
IAO:0000640 |
IAO:0000112 |
Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):
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 |
summary@en |
| 11 |
WARN |
duplicate_exact_synonym |
IAO:0000615 |
IAO:0000118 |
summary@en |
| 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 |