Skip to content

Instantly share code, notes, and snippets.

View mdoering's full-sized avatar

Markus Döring mdoering

View GitHub Profile

Configs & UI

Sector Configs

  • split sectors by code, e.g. IUCN
  • configs, notes
  • search for attach sectors, show FADA Moinidae placed in infra/suborder
  • priority
  • ITIS, WCVP, WoRMS again. Reuse base decisions (search for WCVP), but not for WoRMS which are separate datasets.
    • block or update decision (author, status change)
  • sector publisher
@mdoering
mdoering / xrelease-demo-cfg.yaml
Last active April 3, 2024 13:41
XRelease demo config
# parts of this extended COL checklist configuration was copied from the backbone configs:
# https://github.com/gbif/gbif-configuration/blob/master/cli/nub/config/clb-nub.yaml
# dataset metadata with project variables to be applied to each release
alias: "MD-{attempt}"
title: Merge Demo
version: "{attempt}"
# taxon to use for incertae sedis names during merges
incertaeSedis:
@mdoering
mdoering / reference.bib
Last active October 30, 2023 10:13
TextTree example with properties
@book {SysNat,
author = "Carl Linnaeus",
title = "Systema naturae : per regna tria natura, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis.",
publisher = "Impensis direct. Laurentii Salvii",
address = "Holmiae (Stockholm)",
year = 1766,
volume = 1,
edition = "12th",
pages = {1--532}
}
@mdoering
mdoering / crossref-csl.json
Created October 12, 2023 05:11
crossref csl-json example
{
"DOI": "10.1007/s00705-021-05156-1",
"ISSN": [
"0304-8608",
"1432-8798"
],
"URL": "http://dx.doi.org/10.1007/s00705-021-05156-1",
"alternative-id": [
"5156"
],
alias: "XTEST-{date,yyyy-MM-dd}"
title: XRelease Test
version: "{date,yyyy-MM-dd}"
description: Testing the XRelease feature of ChecklistBank
# taxon to use for incertae sedis names during merges
incertaeSedis:
name: incertae sedis
rank: unranked
status: PROVISIONALLY_ACCEPTED
@mdoering
mdoering / clb-nub.yaml
Created August 22, 2023 08:00
nub config 2023
autoImport: true
validate: false
runAssertions: false
groupBasionyms: true
keepLonelyAutonyms: false
keepEmptyImplicitNames: false
blacklist:
- Calendrella cinerea ongumaensis # https://github.com/gbif/checklistbank/issues/47
- Tricholaema leucomelan namaqua # https://github.com/gbif/checklistbank/issues/46
fdfdfdfd
fdfddf
@mdoering
mdoering / aster-xrel.yaml
Created March 15, 2023 13:40
Aster configs
alias: "XAST{attempt}"
title: Extended Asterales
version: "{attempt}"
description: |
The World Plants and WCVP Asterales order extended by various merge sectors to increase coverage
and test system behavior.
# GBIF publisher keys to follow and create sectors for if missing
sourcePublisher:
# - bb922300-7ddb-11de-a300-90ac77aa923f # Plazi
@mdoering
mdoering / metadata.yml
Created November 10, 2022 09:15
WoRMS Foraminifera Version / Issued ver. (11/2022) / 2022-11-01
---
title: 'World Foraminifera Database'
alias: 'WoRMS Foraminifera'
description: "This World Database of all species of Foraminifera ever described, is part of the World Register of Marine Species (WoRMS), a global initiative to provide a register of all marine organisms.\r\nForaminifera (‘hole bearers’) or forams for short, are a large phylum of amoeboid protozoans (single celled) with reticulating pseudopods, fine strands of cytoplasm that branch and merge to form a dynamic net. They usually produce a test (or shell) which can have one or more chambers, and are made of calcium carbonate (CaCO3) or mineral grains or other particles glued together. The tests are usually less than 0.5 mm in size, but the largest can be up to 20 cm across. Foraminifera are among the most abundant and scientifically important groups of marine organisms. The tests of recently dead planktic foraminifera are so abundant that they form a thick blanket over one third of the surface of the Earth (as Globigerina ooze on the ocean floo
@mdoering
mdoering / col-metadata.json
Created August 5, 2021 16:01
COL Release Metadata
{
"created":"2021-07-29T09:24:54.644871",
"createdBy":101,
"modified":"2021-08-03T07:01:02.918149",
"modifiedBy":101,
"key":2328,
"sourceKey":3,
"type":"taxonomic",
"origin":"released",
"attempt":50,