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task #9940

open

Handle type category formatting in compact typification strings

Added by Andreas Müller about 2 years ago. Updated about 1 month ago.

Status:
In Progress
Priority:
New
Category:
cdmlib
Target version:
Start date:
Due date:
% Done:

60%

Estimated time:
Severity:
normal

Description

In #6865 a separator was added between collection code and collection number.

For single derived units an according formatting was implemented. As described in #6865#note-11 the formatting strategy used there is not well applicable for compact type strings that include typification information (e.g. "holotype") and duplicates (e.g. holotype + isotype) in 1 line.
Therefore we need a different formatting strategy.

Formatting suggestions were made in the early ticket #461. However, none of these examples includes collection code AND accession number (except for the example by IB in #461#note-13 which uses abbreviated type categories such as ST for syntype which do not require a trailing colon but are not well accepted by others).

Another suggestion (by FdAC) was to put the type category behind collection code/number separated by comma (#461#note-27).

The problem is partly solved if the main typification (e.g. holotype) is put in front as suggested in in #461#note-6. However, this does not solve the problem if >1 types are mentioned in the string as e.g. for the syntypes we still need a separator.

Compact type formatting is done in the TypeDesigantionWorkingsetFormatter class. (#9596)


Related issues

Related to EDIT - feature request #461: Improve / compact display of typesIn ProgressAndreas Müller

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Related to EDIT - feature request #2506: (Type-) Specimens may need statusClosedAndreas Müller

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Related to EDIT - task #9941: [DISCUSS] Formatting of type designation categories in compact type stringIn ProgressAndreas Müller

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Related to EDIT - feature request #7081: Deduplicate type information in dataportal if 2 equal types existNewAndreas Müller

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Related to EDIT - bug #6297: [Overview] BGBM User group wishes 2017NewAndreas Müller

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Related to EDIT - feature request #9596: Open issues for TypeDesignationWorkingSetIn ProgressAndreas Müller

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Has duplicate EDIT - feature request #9937: Separator for code and accession number in TypeDesignationWorkingsetFormatterDuplicateAndreas Müller

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Copied from EDIT - feature request #6865: [DISCUSS] Separator for Code and Accession NumberClosedAndreas Müller

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Actions #1

Updated by Andreas Müller about 2 years ago

copied from #6865:

AM:

ein kleiner Nachtrag hierzu:

das Ticket ist jetzt gefixt und das Ergebnis kommt mit dem nächsten Release. Allerdings gibt es bei der kondensierten Darstellung von Typen noch Unklarheit.
Also z.B.
Timaviella dunensis Mikhailyuk & O.Vinogr. – Type: Germany, The coast of the Baltic Sea, Usedom Island, vicinity of Zempin, 54°4'17"N, 13°58'4"E, 8 Oct 2013. (holotype: KW KW-A-32531)

Quelle: https://www.phycobank.org/cdm_dataportal/name/71898bd8-1a6c-42e7-9838-3a1600299ab9/null/null/

Wenn wir hier hinter das erste KW auch einen Doppelpunkt setzen, sieht das seltsam aus.
Gibt es dafür Vorschläge, wie man es besser machen kann?
Das wäre auch für die in Zukunft noch zu optimierende Darstellung von Typusbelegen auf den Taxonseiten relevant.

Actions #2

Updated by Andreas Müller about 2 years ago

  • Has duplicate feature request #9937: Separator for code and accession number in TypeDesignationWorkingsetFormatter added
Actions #3

Updated by Andreas Müller about 2 years ago

Actions #4

Updated by Andreas Müller about 2 years ago

Actions #5

Updated by Andreas Müller about 2 years ago

  • Description updated (diff)
Actions #6

Updated by Andreas Müller about 2 years ago

  • Tags changed from specimen, formatting, type designation to specimen, formatting, type designation, phycobank
Actions #7

Updated by Andreas Müller about 2 years ago

Actions #8

Updated by Andreas Müller about 2 years ago

  • Copied to bug #6297: [Overview] BGBM User group wishes 2017 added
Actions #9

Updated by Andreas Müller about 2 years ago

Actions #10

Updated by Andreas Müller about 2 years ago

  • Related to task #9941: [DISCUSS] Formatting of type designation categories in compact type string added
Actions #11

Updated by Andreas Müller about 2 years ago

AM:

Auch wenn wir die spezifische Typuskategorie nach vorne ziehen (#9941) bleibt das Problem für z.B. Syntypen ja bestehen. Welche Lösung könntet ihr euch dafür vorstellen?

Im Appendix IV des Codes (https://naturalhistory2.si.edu/botany/codes-proposals/display_new.cfm) gibt es die Lösung die auch Norbert vorgeschlagen hat, nämlich zur Trennung zwischen Collection Code und Accession Number „barcode“ oder „No.“ Zu verwenden. Wirklich schön ist das m.E. nicht da sehr unruhig, aber zumindest ist es klar. Gibt es andere gängige Lösungen? Wie wäre es mit Bis-Strich als Separator nach der Typuskategorie?

Actions #12

Updated by Andreas Müller about 2 years ago

  • Subject changed from Handle type category formatting and collection code<->accession number separation in compact typification strings to Handle type category formatting in compact typification strings
Actions #13

Updated by Andreas Müller about 2 years ago

  • Related to feature request #7081: Deduplicate type information in dataportal if 2 equal types exist added
Actions #14

Updated by Andreas Müller about 2 years ago

  • Copied to deleted (bug #6297: [Overview] BGBM User group wishes 2017)
Actions #15

Updated by Andreas Müller about 2 years ago

Actions #16

Updated by Andreas Müller about 2 years ago

  • Related to bug #6297: [Overview] BGBM User group wishes 2017 added
  • Related to feature request #9596: Open issues for TypeDesignationWorkingSet added
Actions #17

Updated by Andreas Müller about 2 years ago

WHK:

eine Doppelung, wie in dem Beispiel ist nicht sehr häufig. Theoretisch könnte man den Herbariumcode in Fett ausgeben, wie das in einigen Journals gemacht wird, dazu würde ich aber gerne die Meinung meiner Kolleg:innen hören.

Actions #18

Updated by Andreas Müller over 1 year ago

  • Assignee changed from Andreas Müller to Belen Escobari
  • Target version changed from Release 5.45 to Release 5.44
Actions #19

Updated by Andreas Müller over 1 year ago

NoK:

all,

I strongly prefer the style with the main typification put in front because this is the least redundant one. Regarding the separator issues I meanwhile find the solution most agreeable that has been agreed on by the Editors of the Code, consistently used since some years in the Appendages of the Code, and has been taken over lately also by Willdenowia.
I think it would in fact make some sense to follow a style that is used by an authoritative source as the Code.

Here two examples from https://doi.org/10.3372/wi.52.52103

Holotype: Peru, Amazonas, Prov. Bongará, Dist. Yambrasbamba, Inmediaciones de la Estación Biologica Abra Patricia, 05°41′32.91″S, 77°48′41.1″W, 2320 m, 19–20 Feb 2020 (fl., fr.), R. Fernandez-Hilario, R. Villanueva & L. Pillaca 1930 (MOL barcode 000006!; isotypes: CUZ!, HOXA accession no. 077852!, NY barcode 04239398!, UPCB accession no. 99400!).

Holotype: Ecuador, Prov. Tungurahua, Cantón Baños, Parroquia Río Negro, Sector El Topo, Estación Cientifica Río Zuñac, Fundación EcoMinga, 01°22.593′S, 78°09.213′W, 1568 m, 26 May 2018 (fl., fr.), L. Jost, F. Recalde & S. Recalde 10600 (QCNE barcode 243978 [1/2], QCNE barcode 243977 [2/2]; isotype: QCNE barcode 243976)

Applied to a B example this would read:
Holotype: Borneo, Sabah, Sandakan Ramos 1490 (B barcode B 10 0018600 (presumed destroyed); isotypes: L, PNH).

Here an example from the Code Appendage, showing how this style handles more complicated cases (with icons as types and epitypes):

Fucus serra S. G. Gmel., Hist. Fuc.: 150. 1768 (Gelidium serra (S. G. Gmel.) E. Taşkin & M. J. Wynne).
Lectotypus (vide Taşkin & Wynne in Webbia 68: 22. 2013): [icon in] Buxbaum, Pl. Min. Cogn. Cent. 2: t. 8, fig. 3, 1728. Epitypus (vide Taşkin & Wynne in Webbia 68: 22. 2013): France, Pyrenées-Orientales, Banyuls-sur mer, Cap Beár, 29 Aug 1932, Feldmann (MICH).

(cont.):

Link for (stable) URI to digital representation of type specimens:

The specimen URI should be linked through the herbarium code (if no barcode or acc. number etc. available) or the entire expression (exemplified in blue):
Holotype: Peru, Amazonas, Prov. Bongará, Dist. Yambrasbamba, Inmediaciones de la Estación Biologica Abra Patricia, 05°41′32.91″S, 77°48′41.1″W, 2320 m, 19–20 Feb 2020 (fl., fr.), R. Fernandez-Hilario, R. Villanueva & L. Pillaca 1930 (MOL barcode 000006; isotypes: CUZ, HOXA accession no. 077852, NY barcode 04239398, UPCB accession no. 99400).

Actions #20

Updated by Andreas Müller over 1 year ago

AM

vielen Dank für die Anmerkungen. Ich habe das auch so in Erinnerung und wir werden versuchen es so zu formatieren.

Wegen den Links: das müsste konfigurierbar werden. Grundsätzlich versuchen wir Links im CDM ja eher hinter die entsprechende Information als Icon zu setzen, statt den Text selber zu verlinken. Da hat man sonst zu viele Links. Zudem ist immer die Frage, ob man direkt auf die externe Quelle verlinken will oder erst auf die CDM Specimen Page. Da gibt es auch unterschiedliche Ansprüche je nach Kontext. Wie gesagt, dass sollte konfigurierbar werden und ist dann sicherlich das Finetuning nach der Gesamtumstellung.

Actions #21

Updated by Andreas Müller over 1 year ago

By the way, the above notes from NoK are also handled in #9941 which is partly a duplicate for this ticket.

Actions #22

Updated by Andreas Müller about 1 year ago

NoK:

Links als icon, ja stimmt ist besser. (Note by AM: later we discussed and checked on other pages that this is not always true and that icon are often used additionally to links but not as the only link)

Linkziel: Sollte mindestens konfigurierbar sein. Ich sehe schon 2 unterschiedliche Kontexte für Specimens. (1) Aus der Synonymie heraus, wo ich bereits eine Typus-Specimen-Zitat habe, will ich den Scan sehen und ggf. reinzoomen und nicht noch mal standardmäßig auf eine Specimen-Seite verwiesen werden (v.a. wenn ich aus dem Link gar nicht sehen kann, ob es dazu überhaupt einen Scan gibt!), wo dann im Normalfall nur dasselbe steht und ich noch einen weitere Klick brauche, um endlich den Scan zu sehen. (2) Aus dem Specimen-Tab heraus, wo ich sofort sehe, ob und welche Zusatzdaten noch existieren, ist es dagegen unbedingt sinnvoll (erst) auf die Specimen-Page zu kommen.

Actions #23

Updated by Andreas Müller 2 months ago

  • Assignee changed from Belen Escobari to Andreas Müller
  • Target version changed from Release 5.44 to Release 5.43

This is closely related to switching to the new taxon pages. Therefore move it to current milestone.

Actions #24

Updated by Andreas Müller about 1 month ago

  • Status changed from New to Resolved
  • % Done changed from 0 to 70

Implemented for new taxon pages.

Actions #25

Updated by Andreas Müller about 1 month ago

  • Status changed from Resolved to In Progress
  • % Done changed from 70 to 60

... maybe some minor issues are still open

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