Term submission - annotation property consider

[zhengj2007]

From @zhengj2007 on July 31, 2015 20:40

From shahid.m...@gmail.com on February 01, 2011 11:41:17

Please indicate the label for the new term consider Please provide a textual definition An annotation property that connects a deprecated information artifact to an information artifact that can be used in its place Please add an example of usage for that term Please provide any additional information below. (e.g., proposed position in the IAO hierarchy) This term is to be used as Annotation Property

comment: contrast with IAO_0100001 (replaced_by), which should only be used when the replacement can be made automatically def_xref: http://wiki.geneontology.org/index.php/Curator_Guide:_Obsoletion#Alternatives_for_Obsolete_Terms , http://www.geneontology.org/GO.format.obo-1_4.shtml xref: obo-format:consider

Original issue: http://code.google.com/p/information-artifact-ontology/issues/detail?id=90

Copied from original issue: information-artifact-ontology/IAO#90

[zhengj2007]

From mcour...@gmail.com on February 01, 2011 11:03:35

Current definition for "term replaced by" reads "Use on obsolete terms, relating the term to another term that can be used as a substitute". Could you provide a definition that makes clear what the differentia is with your term?

Based on what I understood, consider indicates a possible "approximate" replacement, so users should check whether their term was used to denote the same thing than the one referred to by the new class.

If that is correct, maybe something along the lines of "An annotation property that connects a deprecated term to a term that may be used in its place but does not denote the exact same entity" with an editor note indicating "users are advised to review the definition of the new term and check that it matches their intended use" and an example of usage such as the links you point to? (just for the record: we don't use def_xref but instead definition_source, however I don't think this is an issue here. I see that you submitted xref on a different ticket, thanks!)

Summary: Term submission - annotation property consider

[zhengj2007]

From cmung...@gmail.com on February 01, 2011 15:11:04

the new definition and comment looks fine

[zhengj2007]

From alanruttenberg@gmail.com on February 02, 2011 22:43:01

Several issues 1) consider isn't a proper name of a relation as the subject isn't a term - it is a person. How about "term possibly replaced by"? 2) Some obsolescence reasons seemingly shouldn't be used with it and possibly some should be added. 'failed exploratory term' - yes 'placeholder removed' - yes 'terms merged' - no (would be a replaced by) 'term imported' - no (would be replaced by) 'term split' - yes 'other' - don't get me started Please verify, and submit other obsolescence reasons you have encountered, please. 3) Should the documentation here match what is in the OBO format doc? I think it will be confusing if not.

[zhengj2007]

From cmung...@gmail.com on February 02, 2011 22:57:08

not sure I understand (1): "the subject isn't a term - it is a person"? however, "term possibly replaced by" sounds good.

(2) I think every ontology I've every worked with the reason would always be "other".

'failed exploratory term' - I've never seen an exploratory term 'placeholder removed' - I maybe recall these from the early obi days, but otherwise never seen 'terms merged' - in obo-format, merged terms are not obo-format-obsolete. however, we could consider changing the mapping such that alt_ids generate deprecation annotation assertions 'term imported' - is there more docs on this? is this owl-imported, or mireot/merged? 'term split' - ok, I've seen this a lot

for more on current usage see: http://wiki.geneontology.org/index.php/Curator_Guide:_Merge_Split_Move http://wiki.geneontology.org/index.php/Curator_Guide:_Obsoletion I wasn't aware there was a vocabulary of obsoletion reasons in IAO. Did anyone do a survey of the current usage, e.g. in GO?

[zhengj2007]

From alanruttenberg@gmail.com on February 02, 2011 23:33:46

explanation: if you write the (semi english) X consider Y, then what sort of thing is X? The sort of thing that can consider. A person. An editor. Not a term.

No survey of GO. Would be nice to have, as would the Werner reasons. Melanie like these things - talk to her?

term imported: editor note: "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." rtfo ;-)

'other' is about to be deprecated. obsolescence reason: failed exploratory term.

[zhengj2007]

From mcour...@gmail.com on February 22, 2011 10:05:12

As far as I remember the original list of obsolescence reasons was based on Werner's paper (there is an editor note "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.") I'd be happy to hear if other values are needed.

Proposal: label: term possibly replaced by def: An annotation property that connects a deprecated term to a term that may be used in its place but does not denote the exact same entity editor note:users are advised to review the definition of the new term and check that it matches their intended use editor note: contrast with IAO_0100001 (replaced_by), which should only be used when the replacement can be made automatically example of usage: http://wiki.geneontology.org/index.php/Curator_Guide:_Obsoletion#Alternatives_for_Obsolete_Terms example of usage: http://www.geneontology.org/GO.format.obo-1_4.shtml definition source: obo-format:consider