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task #7012

task #6168: Full registration workflow model

Workflow with Pensoft

Added by Andreas Kohlbecker almost 2 years ago. Updated 6 months ago.

Status:
In Progress
Priority:
New
Category:
Workflow
Start date:
10/09/2017
Due date:
% Done:

0%


Description

Design and establish an partially automated workflow with Pensoft.


The below concept is based on a discussion with Teodor Georgiev (preprint@pensoft.net) from Pensoft Publishers at the TDWG 2017 conference.

Interaction workflow between Phycobank and Pensoft Publishers

Phycobank is a repository for registration of algal names and types according to the International Code of Nomenclature for algae, fungi, and plants (ICN). Phycobank will actually create registration for whole nomenclatural acts which can encompass 0 - 1 new scientific names and 0 - n typifications for new or existing names. The different types of typifications cover isosyntype, isotype, lectotype, neotype, paralectotype, paraneotype, paratype, second step lectotype, second step neotype & syntype.

Phycobank aims in establishing a workflow with publishers. Phycobank aims in realizing this interaction for the first time with Pensoft Publishers.

he basic principles of the interaction between Phycobank and Pensoft Publishers as described in this document have been discussed during the "Night at the museum" event at the TDWG conference 2017 (Andreas Kohlbecker, a.kohlbecker@bgbm.org; Teodor Georgiev, preprint@pensoft.net). The current state of this concept is more elaborated and detailed in contrast to the outcome of the discussion in Ottawa on October, 2017 which has been sent to preprint@pensoft.net on Oktober 10th 2017

persistent registration identifier

For interaction with registration web service persistent registration identifier ({phycobankID}) needs to be used in the request URI as url-encoded path element: {phycobankID-urlencoded} = urlencode(http://phycobank.org/{integer})

Authentication/authorization

The Publisher will need to authenticate at the Phycobank registration webservice via HTTP-Basic authentication. Authorization at Phycobank is established on base of the OAuth 2.0 protocol.

Users and roles

Phycobank distinguishes two roles which are relevant for the registration process:

  • Submitter: The user initiating a registration is called submitter. Only the submitter of a registration can modify the related data. There is always only one submitter per registration. Pensoft will therefore be the submitter of all registrations created on behalf of the authors which do submit publications to Pensoft witch contain nomenclatural acts for algae names.
  • Curation: The curation of Phycobank can also modify registration data as long the registration is not yet published.

Registration workflow states

  • PREPARATION: Initial state of a new registration
  • CURATION: Once the editing phase of a nomenclatural act is completed, the registration record (new scientific name, typifications) are passed to the curation. This status indicates that a registration is in the curatorial process. As result of this process (for details see paragraph below) the status may be changed to READY, REJECTED (severe unsolvable problem with the nomenclatural act) or even back to PREPARATION (request to fix incomplete, invalid data)
  • READY: The registration record can be published. The publication will immediately happen as soon as the publication date (, doi and pages detail) is set in the data.
  • PUBLISHED: Unmodifiable final state of a successful registration. All related data is locked and can no longer be modified.
  • REJECTED: Unmodifiable final state of a failed registration. All related data is locked and can no longer be modified.

Curatorial process in the registration office

The data curator of the registration office will manually validate the registration data once the status is set to CURATION. The curation process may result in one or more of the following actions:

  • Minor problems in the data are corrected by the curator. This includes for example minor orthographic corrections of a new name to be published, atomize specimen data, if necessary; add missing data (e.g. publication date of basionym reference).
  • Severe problems like that the exact same name has already been published before will lead to rejection of the registration which is expressed by the state REJECTED
  • The registration state is progressed to READY in case of successful validation.
  • The state returns to PREPARATION in case of problems which can't be solved by the curator without feedback from the author team. The curator will add a curatorial annotation to the registration record with information or questions for the author team. TODO: This needs to be discussed #8103

Initialization of the registration process

The initialization of the registration process is triggered by the publisher by sending nomenclatural act data to the registration system via HTTP POST request:

Upon being authenticated the publisher can send the data of the nomenclatural act (Name, Types, Reference ) to a web service endpoint ( ==> #8086). The model of the data is currently being developed ==> #8085. For an brief overview on the required data and its granularity, please see the paragraph Data scope and granularity below

As response to the submission the publisher will receive a response object (==> #8086) which can contain:

  • An HTTP error code (400) with a detailed error message in case the submitted data was causing a problem in the Phycobank system.
  • The persistent identifier (http://phycobank.org/{integer}) for the nomenclatural act. The identifier and according registration is not made public at this point.
  • The current status of the registration. Initially this is PREPARATION

Data scope and granularity

(For a detailed discussion on this topic please see #8085)

Pyhcobank is a registration for nomenclatural acts. There are two general types of acts to be distinguished:

  1. New name + one or more typifications (The new name is the typified name in this case)
  2. One or more typification for an name which has previously been published in an other publication.

(Required fields are marked with an asterisk * in the below listings)

Name

A name can have different roles in a nomenclatual act:

  1. it is the name being newly published
  2. it is the name for which a typification is published, in this case the name is the typified name (specimen types and name types)
  3. it is used in a typification as type for another name, in this case the name is the type name (name types).
  4. it related to a name used in the cases 1) to 3) as basionym, replaced synonym, validated name or orthographcally corrected name.
  • genusOrUninomial*:
  • specificEpithet*:
  • rank*:
  • nameType*: (="ICNAFP"),
  • nomenclaturalReference*:
  • citationDetail*:
  • nameRelationships: (relations to other name which are basionym, replaced synonym, validated name or orthographcally corrected name.)

Typifications

Specimen types

  • summary text*: e.g.
    • C Ghana 141/1961. “Southwest Ghana. Fresh water (a small stream in bamboo thicket between the villages Agona and Nsuaem, Loc. No. 12). 9.III.1961.”
    • NMW C90.12.179 “River Chigara, Sierra Leone”
  • type status*: (holotype, lectotype, ...)
  • kind of unit*: (="Specimen")
  • record basis*: (="PreservedSpecimen")
  • collection code* : Index Herbariorum Code (C, BRM, B, BM or BP etc.)
  • accession number*: e.g. C90.12.179
  • typified name*: (a reference to the typified name)

Name types

  • type status*: (e.g. lectotype, original designation, ...)
  • typified name*: (a reference to the typified name)
  • conserved type: [true|false]
  • rejected type: [true|false]
  • not designated type: [true|false]
  • type name*: (a reference to the typified name)
  • citation detail*:

Receiving messages from Phycobank during the edit and curation process

The submitted registration record will undergo a manual curation process which may result in a notifications on the registration record. Notifications may report invalidity of the submitted data and thus may be requests for improving data, fixing problems in the submitted nomenclatural act.

Prospective service endpoint (#7270): rejected, see #7935

For a new concept see #8103

Requesting for the status of a registration record

TODO Can we get rid of the identifier/ in the service URL? We could allow for {uuid} and {phycobankID-urlencoded} in the same place.

response data model

  • The webservice responds with the current status which is one of:
    • CURATION
    • PREPARATION
    • PUBLISHED
    • READY
    • REJECTED

response model ( ==> #8087):

{
    "registrationId" : "{Registration.identifier}"
    "status": "{Registration.status}"
}

Publishing a registration identifier

In order to publish the registration of the nomenclatural act the publisher needs to submit the publication date, DOI and the pages detail to Phycobank.

Once all this information is successfully submitted the registration record can potentially change it's status to 'PUBLISHED'. This will immediately happen if the status is 'READY'. It is not guaranteed that the curation process is finished when publishing details are received, in these cases the registration becomes only public once the curator sets the registration status to 'READY'. The persistent Phycobank identifier will only be resolvable once the registration is in state 'PUBLISHED'. Therefore the publisher could consider to postpone the publication of the article until the registration record in the registration is on state 'READY', otherwise the publication would contain a unresolvable identifier.

HTTP-PUT: http://api.phycobank.org/phycobank/registration/{phycobankID-urlencoded}

Request data which triggers a registration which is READ to change the status to PUBLISHED:

  • publicationDate : the ISO 8601 date (JJJJ-MM-TT) of the actual publication of the article.
  • pages : detail information on the pages covering the published article
  • doi

Workflow as sequence diagram

Open Questions

  • How to deal with new related names? Create blocking registrations?
    • does the publisher need to deal with blocking registrations explicitely or is this been managed behind the scenes for him?
  • Discuss: If the object is Multimedia or a strain -> no automatic submission (because this is a different workflow for >5% of the types?
  • How is data exchanged between Pensoft and Mycobank?
  • What is the level of granularity at which Pensoft can deliver data?

sequence-diag-no-curation.png View (72.2 KB) Andreas Kohlbecker, 02/12/2019 05:03 PM

digital publisher workflow - webservices.xmi (45.1 KB) Andreas Kohlbecker, 02/13/2019 06:46 PM

submission and publication with curation.png View (181 KB) Andreas Kohlbecker, 02/20/2019 03:36 PM


Related issues

Related to Edit - feature request #7270: Registration message controller implemented Rejected 02/15/2018
Related to AlgenRegistrierung - feature request #8103: Feedback mechanism from curator to publisher and author team Rejected 02/15/2019
Related to Edit - feature request #8086: registration submission endpoint implemented New 02/08/2019
Related to Edit - feature request #7927: Registration not found, Portal handling registrations in preparation Closed 11/26/2018
Related to Edit - task #8087: improve response model of registration/identifier/{registrationID}/status.json web service New 02/08/2019
Related to AlgenRegistrierung - task #8085: Decide on a data schema to use for submitting nomenclatural acts to the cdm web service New 02/08/2019

History

#1 Updated by Andreas Kohlbecker almost 2 years ago

  • Description updated (diff)

#2 Updated by Andreas Kohlbecker almost 2 years ago

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#3 Updated by Andreas Kohlbecker almost 2 years ago

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#4 Updated by Andreas Kohlbecker almost 2 years ago

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#5 Updated by Andreas Kohlbecker almost 2 years ago

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#6 Updated by Andreas Kohlbecker almost 2 years ago

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#7 Updated by Andreas Kohlbecker almost 2 years ago

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#8 Updated by Andreas Kohlbecker almost 2 years ago

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#9 Updated by Andreas Kohlbecker almost 2 years ago

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#10 Updated by Andreas Kohlbecker almost 2 years ago

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#11 Updated by Andreas Kohlbecker almost 2 years ago

  • Category set to Workflow
  • Status changed from New to In Progress
  • Assignee set to Andreas Kohlbecker

#12 Updated by Andreas Kohlbecker almost 2 years ago

workflow draft sent to Teodor Georgiev (preprint@pensoft.net) per email

#13 Updated by Andreas Kohlbecker over 1 year ago

  • Description updated (diff)

#14 Updated by Andreas Kohlbecker over 1 year ago

#15 Updated by Andreas Kohlbecker 6 months ago

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#16 Updated by Andreas Kohlbecker 6 months ago

  • Target version set to Digital Publisher Workflow

#17 Updated by Andreas Kohlbecker 6 months ago

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#18 Updated by Andreas Kohlbecker 6 months ago

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#19 Updated by Andreas Kohlbecker 6 months ago

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#20 Updated by Andreas Kohlbecker 6 months ago

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#21 Updated by Andreas Kohlbecker 6 months ago

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#22 Updated by Andreas Kohlbecker 6 months ago

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#24 Updated by Andreas Kohlbecker 6 months ago

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#25 Updated by Andreas Kohlbecker 6 months ago

workflow with publisher modeled as UML sequence diagram in Umbrella

#26 Updated by Andreas Kohlbecker 6 months ago

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#27 Updated by Andreas Kohlbecker 6 months ago

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#28 Updated by Andreas Kohlbecker 6 months ago

  • File submission and publication with curation.png added
  • Description updated (diff)

updating the workflow with curatorial review

#29 Updated by Andreas Kohlbecker 6 months ago

  • File submission and publication with curation.png added

higher dpi: 96

#30 Updated by Andreas Kohlbecker 6 months ago

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#31 Updated by Andreas Kohlbecker 6 months ago

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#32 Updated by Andreas Kohlbecker 6 months ago

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#33 Updated by Andreas Kohlbecker 6 months ago

  • File submission and publication with curation.png added

120 dpi

#34 Updated by Andreas Kohlbecker 6 months ago

  • Description updated (diff)

#35 Updated by Andreas Kohlbecker 6 months ago

  • File submission and publication with curation.png added

96dpi

#36 Updated by Andreas Kohlbecker 6 months ago

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#37 Updated by Andreas Kohlbecker 6 months ago

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#38 Updated by Andreas Kohlbecker 6 months ago

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#39 Updated by Andreas Kohlbecker 6 months ago

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#40 Updated by Andreas Kohlbecker 6 months ago

#41 Updated by Andreas Kohlbecker 6 months ago

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#42 Updated by Andreas Kohlbecker 6 months ago

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#43 Updated by Andreas Kohlbecker 6 months ago

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#44 Updated by Andreas Kohlbecker 6 months ago

#45 Updated by Andreas Kohlbecker 6 months ago

  • Related to feature request #7927: Registration not found, Portal handling registrations in preparation added

#46 Updated by Andreas Kohlbecker 6 months ago

  • Related to task #8087: improve response model of registration/identifier/{registrationID}/status.json web service added

#47 Updated by Andreas Kohlbecker 6 months ago

  • Description updated (diff)

#48 Updated by Andreas Kohlbecker 6 months ago

  • Related to task #8085: Decide on a data schema to use for submitting nomenclatural acts to the cdm web service added

#49 Updated by Andreas Kohlbecker 6 months ago

  • Description updated (diff)

#50 Updated by Wolf-Henning Kusber 6 months ago

Specimen type:
default could be "specimen"

Fill in automatically by the publisher mandatory fields:
Select type (e.g. holotype)
Index Herbariorum Code (BRM or B or BM or BP etc.)

Put in type information into the Cache field
Discuss: If the object is Multimedia or a strain -> no automatic submission (because this is a different workflow for >5% of the types?

#51 Updated by Andreas Kohlbecker 6 months ago

  • Description updated (diff)

#52 Updated by Andreas Kohlbecker 6 months ago

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#53 Updated by Andreas Kohlbecker 6 months ago

  • File submission and publication with curation.png added

updating diagram with corections. (96dpi)

#54 Updated by Andreas Kohlbecker 6 months ago

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#55 Updated by Andreas Kohlbecker 6 months ago

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#56 Updated by Andreas Kohlbecker 6 months ago

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#57 Updated by Andreas Kohlbecker 6 months ago

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#58 Updated by Andreas Kohlbecker 6 months ago

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#59 Updated by Andreas Kohlbecker 6 months ago

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#60 Updated by Andreas Kohlbecker 6 months ago

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#61 Updated by Andreas Kohlbecker 6 months ago

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#63 Updated by Andreas Kohlbecker 6 months ago

  • File deleted (submission and publication with curation.png)

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