sprint 6: topics to be covered

[myrmoteras]

Topics for sprint 6

BLR

Create a UI for the BLR community making use of the new EU portal

• create a mockup (before the sprint) (see issue)
• integrate or discuss the role the search functionality in https://plazi.org/litsearch/

Workflow BLR - SiBILS / Biodiversity PMC

Define the upload of BLR/Zenodo communities to Biodiversity PMC [Notes], Pipeline Arcadia Sprint: Zenodo - BLR pipeline

• Article JATS
• Plazi to bPMC
  • Avoid duplication when updating bPMC
• Floras to be added to bPMC
• Onboarding the many collections
  • Taxodros
  • Bats
  • Phytochemistry
  • EJT
  • (Wiley. Frontiers)
  • [...]
• Zenodo to bPMC
• Plazi to Zenodo
• bPMC to Zenodo - based on URL

Creating communities and batch upload

Finish Lycophron uploads

• for articles, including retrieving the Zenodo DOI and means to update metadata. assure that POA can handle the upload
• upload of physical objects linked to figures and other data, means to update data. Get the MfN upload to work routinely.

Post Arcadia

Discuss Post Arcadia

[myrmoteras]

Plazi Administration

• domain name management

[flsimoes]

TreatmentBank, GoldenGate, IMF development

• Controlled type vocabulary for table columns
  • https://github.com/plazi/Plazi-Communications/issues/1231
• Document categories (projects, qc tags, etc)

[asrivathsan]

Batch upload

Lycophron

repo

• simple upload (e.g. corpus of publications)

• combined upload (e.g. physical object * image)

• finish programming

• document so somebody in Plazi could operate

For the MfN upload the key issues:

• Workflow for barcode data (Batch CSV)

• trigger creation of new physical object
• Add to existing physical object
• Ability to flag a contamination
• Add link to MinION sequencing run DOI for barcode

• Create link for sequenceID (GBIF) for barcode and possible "Google lens" for image
• Compatibility of existing image workflow and barcode workflow
• Ensure existence of Collection event (e.g. https://sandbox.zenodo.org/records/108687) before creation of any physical object DOI.
• Return of Zenodo ID upon upload
• Fix existing links in MfN phyisical objects to direct links instead of search terms (see example: https://sandbox.zenodo.org/records/115781)

[myrmoteras]

Annotations: WADM upload from TB to BLR

• Define elements to upload
• Create upload and test

[myrmoteras]

Tables

• define table data types (columns)
• table treatments / material citations
• add attributes in table to create complete material ciations

[myrmoteras]

Various open bilateral issues TB / Zenodo

• list provided by @gsautter for discussion with @slint

[myrmoteras]

Bilateral Issues Plazi / SIBiLS

• Metaplantcode related issues
• Installing a TreatmentBank instance on SIBiL server

[gsautter]

Various open bilateral issues TB / Zenodo

* list provided by [@gsautter](https://github.com/gsautter) for discussion with [@slint](https://github.com/slint)

This mainly concerns which HTML tags and attributes are permitted in the description of depositions, specifically tags and attributes required to properly display tables.

[gsautter]

Another topic will most likely be sorting out any open JATS export issues with @tcatapano

[myrmoteras]

DCL ingest into TB

prepare to ingest the DCL documents into TB.