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Ontologies for use in representing data from taxonomic treatments in RDF
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extracted nomenclatorial terms #37

Open myrmoteras opened 1 year ago

myrmoteras commented 1 year ago

via @tcatapano
the terms and their definitions in the taxonomic_nomenclatural_status_terms.owl ontology by Paul Morris as basis for further discussions

nomenclatorial terms

lyubomirpenev commented 1 year ago

@myrmoteras Can you send me the list of nomenclatural terms of Bob Morris please? @gsautter @retog is there a reconciled list of nomenclatural terms used in legacy literature (e.g. sp. n. = spec. n., species nova, sp. nov., etc.)? It would be good to align the reconciled terms used by Plazi and Pensoft

myrmoteras commented 1 year ago

@lyubomirpenev the terms are listed at the begin of this issue.

Yes, we should come up with a standard form for elements like "sp. n." we have been thinking of it, but did not yet follow through (see the terms used). This might be something to ask the community to chip in?

@gsautter have you given this any thought in terms of the big batch?

lyubomirpenev commented 1 year ago

Impressive list which needs to be reconciled (shouldn't take much effort) to a list of standardised terms used by both Plazi and Pensoft. I asked about sharing permission for the Paul Morris's spreadsheet of nomenclatural terms. Is that possible?

gsautter commented 1 year ago

Not only for the Big Batch ... FAT does a lot in this regard to properly tag the taxonomicNameLabels, and the treatment statistics also normalize to some degree to better support aggregation ... a good part of it happens somewhat programmatically, though, so I cannot simply copy&paste a list here ... but here a few general underlying principles:

Also, and that's the programmatic part, "spec." and "nov." and combine to both "spec. nov." and "nov. spec.", with either substituted by either of the alternatives listed above ... would explode into quite the list if all the alternatives were given explicitly in all combinations. Note that this never changes the original text of the publication, but only goes into the status attribute of a preceding taxonomicName, or in the respective fields of the treatment statistics, respectively ... I'm aware the latter do need some cleanup, and in part also the former, and that is planned as part of the Big Batch.

This might not readily be a list to agree upon, but provide a starting point for further discussion.

myrmoteras commented 1 year ago

the point is: we need a "canonical" for for new species that we use in out attributes. Eg.

sp. nov. = spec. n. = spec. nov. should have the sp.nov. attribute. eg http://webprojects.huh.harvard.edu/ontologies/taxonomic_nomenclatural_status_terms.owl#sp_nov in https://docs.google.com/spreadsheets/d/17UsLQ1iIrr5O2EicC_RtgVKLTF9y1eofp5FO-ARvdwM/edit#gid=476777259 which will lead to out nomenclature ontology we discuss

lyubomirpenev commented 1 year ago

Exactly, but not just for the new species but also for all kind of nomnclatural acts, such as status nova, nomen novum etc. etc.На 13.06.2023 г. 23:37 ч. Donat Agosti @.***> написа: the point is: we need a "canonical" for for new species that we use in out attributes. Eg. sp. nov. = spec. n. = spec. nov. should have the sp.nov. attribute. eg http://webprojects.huh.harvard.edu/ontologies/taxonomic_nomenclatural_status_terms.owl#sp_nov in https://docs.google.com/spreadsheets/d/17UsLQ1iIrr5O2EicC_RtgVKLTF9y1eofp5FO-ARvdwM/edit#gid=476777259 which will lead to out nomenclature ontology we discuss

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