Granularity levels, verification and Quality Control #195

flsimoes · 2022-09-30T15:08:08Z

We need to define what we understand as Granularity, Verification and Quality Control, and what levels to assign to it.
EDIT: QC and Verification are dropped. We'll focus on general granularity + a QCd/Not-QCd tag

Granularity

The level of processing applied to a given document. This is the level to which the batch (or an individual extraction) goes to.
At the moment, processing through batch currently does not enable any partial processing, meaning it activates all the treatment, treatmentCitation, and materialsCitation macros. In order to apply the levels below we would need to implement elements that enables the template creator to signal at what point a batch process should stop.

Level 0
- Objective: Make a document Machine-actionable
- Product:
  - PDF made FAIR and Machine-actionable (e.g. PDF uploaded to BLR/Zenodo)
  - Metadata
- Checked by default (users need to have the correct metadata to upload it)
Level 1
- Objective: Make IMFs available (JATS), document structure, figures and tables
- Product:
  - PDF made Machine-readable
  - Figures
  - Tables
- Checked/Not-Checked: Blocks, paragraphs, line breaks, captions, etc
  - Blocks Transits to: Zenodo, GBIF
- Templated/Not-templated
Level 2
- Objective: Provide taxonomicNames, sections, treatments, subSubSections and references
- Product:
  - treatment
    - nomenclature subSubSections (mandatory)
    - other subSubSections
  - taxonomicNames
  - bibliographic references
- Checked/Not-Checked: boundaries and attributes of subSubSections, taxonomicNames and bibRefs
  - Blocks Transits to:
Level 3 (a, b)
- Objective: Provide treatmentCitations (3a) OR materialsCitations (3b), if both "3"
- Product:
  - treatmentCitations (3a)
  - materialsCitations (3b)
- Checked/Not-Checked: boundaries of treatmentCitations and/or materialsCitations
  - Blocks Transits to:
Level 4
- Objective: Parse treatmentCitations (4a) OR materialsCitations (4b), if both "4"
  - Distinction between types-only and full matCit
- Product:
  - treatmentCitations (4a)
  - materialsCitations (4b)
- Checked/Not-Checked: attributes/parsing of treatmentCitations and/or materialsCitations
  - Blocks Transits to:

(DEPRECATED)

Quality Control

The amount of verification and parsing Plazi applies to a given document. This QC level system is a translation of what we currently dub "Granularity levels"

Level 0 (none)
- No QC protocol carried after standard processing
Level 1 (low)
- Standard QC currently applied to the likes of Zootaxa and Phytotaxa. Plazi only looks at clearing blocker flags to enable publications, treatments and any other product to transit to GBIF, LOD, etc
Level 2 (medium)
- Currently applied to the MNHN journals (Adansonia, Anthropozoologica, Geodiversitas and Zoosystema).
- The new specifications need to be discussed, but it will involve looking at treatments, subSubSections and holotypes.
Level 3 (high)
- Currently applied solely to EJT.
- Highest level of QC, involves checking all treatments, materialsCitations and treatmentCitations.

Verification

The level to which a document has been fully checked by an user. The inspiration for this model is iNaturalist

Not Verified
- Document was processed, but no one made any further checks (QC level 0)
Plazi Verified
Expert Verified
- With this tier we expect to get verification of the accuracy of the extracted data from experts in the related field

flsimoes · 2022-10-03T17:48:35Z

I'm adding the specifications for each level and further descriptions

flsimoes · 2022-10-03T18:17:50Z

@myrmoteras please check it out

flsimoes · 2022-10-04T19:57:00Z

It would also be really useful to have this tags findable through the TB Stats

gsautter · 2022-10-04T20:28:05Z

It would also be really useful to have this tags findable through the TB Stats

Sure thing ... once they are defined and we start assigning them, that is ... beforehand, there's preciously little sense in adding a bunch of empty stats fields.

flsimoes · 2022-10-04T20:39:56Z

It would also be really useful to have this tags findable through the TB Stats

Sure thing ... once they are defined and we start assigning them, that is ... beforehand, there's preciously little sense in adding a bunch of empty stats fields.

Completely agree, and that's why we are here discussing them :)

myrmoteras · 2022-11-07T08:34:58Z

@flsimoes let's define the granularity levels, and let's have 3- 5 "gold standard" publications where we can show this, and which include the variation of treatments, ie

for new species,
redescriptions with treatment citations,
redescriptions with treatment citations including synonymy,
redescriptions with treatment citations including synonymy and links to the cited treatments
complete and less complete material citations.
Articles with 1 to 5 treatments

flsimoes · 2022-11-08T21:30:56Z

We're currently gathering examples

myrmoteras · 2022-11-22T11:29:12Z

example papers:
article stats; treatmentStats; JSON

Cipola, Nikolas G. & Katz, Aron D., 2021, Morphological and molecular analysis of Willowsia nigromaculata (Collembola, Entomobryidae, Entomobryinae) reveals a new cryptic species from the United States, European Journal of Taxonomy 739 (1), pp. 92-116 FFCEFFA71D0DD960FF886D158538FF88
Silva, Ruan Felipe Da, Caron, Edilson & Carvalho-Filho, Fernando Da Silva, 2022, An update on Termitomorpha Wasman (Coleoptera: Staphylinidae) including a new species, species redescriptions and geographic extension, Zootaxa 5205 (1), pp. 1-25
https://tb.plazi.org/GgServer/summary/9F3EB341FFF2FF82B345D672FF811F58
Subedi, Madan, 2022, A new genus and a new groundhopper species from Nepal (Orthoptera: Tetriginae Skejotettix netrajyoti gen. et sp. nov.), Zootaxa 5205 (1), pp. 35-54
https://tb.plazi.org/GgServer/summary/737C7525576CFFF6FFBEFF8F3E49FFC1
Cutrim, Marcelo, M, Alberto, Silva-Neto, oreira da, Rafael, José Albertino, García, Alfonso Nery & Aldrete, 2022, The genus Ptiloneura Enderlein, 1901 (Psocodea, ‘ Psocoptera’, Ptiloneuridae) in the Brazilian Amazon Forest and Atlantic Forest: new species, variations in forewings and a key to the species, Zoosystema 44 (20), pp. 493-501
https://tb.plazi.org/GgServer/summary/244CDA14FFD3BB1B2820FF8C5E190A55
Štepánek, Jan & Kirschner, Jan, 2013, A revision of mountain species of the genus Taraxacum F. H. Wigg. (Compositae) in Corsica, Candollea 68 (1), pp. 29-39
https://tb.plazi.org/GgServer/summary/FFD01C59FFE65F4EBF6AFFD7FFB5CA6C

flsimoes · 2022-11-22T11:34:50Z

We need to flesh out a few things, such as difference between automatic and manual bibRef parsing and level of detail of matCit parsing.

myrmoteras · 2022-11-23T20:36:47Z

@flsimoes here is the milestone "Initial scoping and assessment of optimal degree of automation for processing workflow" i n BiCIKL that deals also with granularity issues.

myrmoteras · 2022-11-28T13:39:37Z

Annotations for level 4, covering treatments, NOT tables yet.

see also Agosti et al, 2022 for further explanation of the annotations.

annotation	Element name	comment
`treatment`	Treatment
`subSubSection`	Treatment sub-sections
`treatmentCitationGroup`	A group of treatment citations for the same taxon concept
`treatmentCitation`	a citation of a previous treatment
`taxonomicName`	Scientific name
`taxonomicNameLabel`	Designator for a new or changed scientific name
`materialsCitation`	Citation of a physical specimen
`collectingCountry`	Country where the specimen has been collected
`location`	location where the specimen has been collected
`date`	Date of the collection of the specimen
`specimenCode`	code assigned to a specimen by an institution
`geoCoordinate`	geographic coordinates
`elevation`	elevation of the collection of the specimen
`collectorName`	person who collected the specimen
`collectionCode`	code of the institution hosting the specimen
`accessionCode`	code of the DNA sequence isolated from the specimen

Nesting of the annotations

The tags have specific positions in a treatment.

annotation	sub-annotation	subsub-annotation	subSubSub-annoation	comment
`taxonomicName`				Scientific name; can occur in all sections, including material citation. Can occur anywhere in a treatment or article
`taxonomicNameLabel`				Designator for a new or changed scientific name
`treatment`
	`subSubSection`			Treatment sub-sections
		`treatmentCitationGroup`		A group of treatment citations for the same taxon concept
		`treatmentCitation`		a citation of a previous treatment can be alone, or nested in TCG
		`materialsCitation`		Citation of a physical specimen
			`collectingCountry`	Country where the specimen has been collected
			`location`	location where the specimen has been collected
			`date`
			`specimenCode`
			`geoCoordinate`
			`elevation`
			`collectorName`
			`collectionCode`
			`accessionCode`

myrmoteras · 2022-11-28T14:45:41Z

example papers: article stats; treatmentStats; JSON

Silva, Ruan Felipe Da, Caron, Edilson & Carvalho-Filho, Fernando Da Silva, 2022, An update on Termitomorpha Wasman (Coleoptera: Staphylinidae) including a new species, species redescriptions and geographic extension, Zootaxa 5205 (1), pp. 1-25
https://tb.plazi.org/GgServer/summary/9F3EB341FFF2FF82B345D672FF811F58
12:28 Uhr

Subedi, Madan, 2022, A new genus and a new groundhopper species from Nepal (Orthoptera: Tetriginae Skejotettix netrajyoti gen. et sp. nov.), Zootaxa 5205 (1), pp. 35-54
https://tb.plazi.org/GgServer/summary/737C7525576CFFF6FFBEFF8F3E49FFC1
12:28 Uhr

Cutrim, Marcelo, M, Alberto, Silva-Neto, oreira da, Rafael, José Albertino, García, Alfonso Nery & Aldrete, 2022, The genus Ptiloneura Enderlein, 1901 (Psocodea, ‘ Psocoptera’, Ptiloneuridae) in the Brazilian Amazon Forest and Atlantic Forest: new species, variations in forewings and a key to the species, Zoosystema 44 (20), pp. 493-501
https://tb.plazi.org/GgServer/summary/244CDA14FFD3BB1B2820FF8C5E190A55

Štepánek, Jan & Kirschner, Jan, 2013, A revision of mountain species of the genus Taraxacum F. H. Wigg. (Compositae) in Corsica, Candollea 68 (1), pp. 29-39
https://tb.plazi.org/GgServer/summary/FFD01C59FFE65F4EBF6AFFD7FFB5CA6C

@flsimoes can you please make sure that these examples are all high level and checked - so they work as examples.

flsimoes · 2022-11-28T14:58:10Z

We'll make sure of that

flsimoes · 2022-11-28T19:01:07Z

All high-level now

flsimoes · 2023-11-01T09:09:08Z

TaxPub - level-1
plazi/ggxml2taxpub#21

flsimoes · 2023-11-01T12:29:38Z

From Patrick Ruch

"The document granularity is one of the subject of BioHackathon n26 that we are organizing; therefore I am cc-ing to Alexandre and Julien for respectively the Elixir BioHackathon, which is currently going on, and the BioC format used in SIBiLS and displayed in Pam's module.

Let's add it to the agenda of thursday !"

flsimoes assigned flsimoes, myrmoteras and Carol-Sokolowicz Sep 30, 2022

flsimoes added the quality control label Oct 4, 2022

flsimoes unassigned Carol-Sokolowicz Nov 22, 2022

myrmoteras mentioned this issue Dec 7, 2022

define tasks for Anestore #201

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Granularity levels, verification and Quality Control #195

Granularity levels, verification and Quality Control #195

flsimoes commented Sep 30, 2022 •

edited

Loading

flsimoes commented Oct 3, 2022

flsimoes commented Oct 3, 2022

flsimoes commented Oct 4, 2022

gsautter commented Oct 4, 2022

flsimoes commented Oct 4, 2022

myrmoteras commented Nov 7, 2022

flsimoes commented Nov 8, 2022

myrmoteras commented Nov 22, 2022 •

edited

Loading

flsimoes commented Nov 22, 2022

myrmoteras commented Nov 23, 2022

myrmoteras commented Nov 28, 2022 •

edited

Loading

myrmoteras commented Nov 28, 2022

flsimoes commented Nov 28, 2022

flsimoes commented Nov 28, 2022

flsimoes commented Nov 1, 2023 •

edited

Loading

flsimoes commented Nov 1, 2023 •

edited

Loading

Granularity levels, verification and Quality Control #195

Granularity levels, verification and Quality Control #195

Comments

flsimoes commented Sep 30, 2022 • edited Loading

Granularity

(DEPRECATED)

Quality Control

Verification

flsimoes commented Oct 3, 2022

flsimoes commented Oct 3, 2022

flsimoes commented Oct 4, 2022

gsautter commented Oct 4, 2022

flsimoes commented Oct 4, 2022

myrmoteras commented Nov 7, 2022

flsimoes commented Nov 8, 2022

myrmoteras commented Nov 22, 2022 • edited Loading

flsimoes commented Nov 22, 2022

myrmoteras commented Nov 23, 2022

myrmoteras commented Nov 28, 2022 • edited Loading

Annotations for level 4, covering treatments, NOT tables yet.

Nesting of the annotations

myrmoteras commented Nov 28, 2022

flsimoes commented Nov 28, 2022

flsimoes commented Nov 28, 2022

flsimoes commented Nov 1, 2023 • edited Loading

flsimoes commented Nov 1, 2023 • edited Loading

flsimoes commented Sep 30, 2022 •

edited

Loading

myrmoteras commented Nov 22, 2022 •

edited

Loading

myrmoteras commented Nov 28, 2022 •

edited

Loading

flsimoes commented Nov 1, 2023 •

edited

Loading

flsimoes commented Nov 1, 2023 •

edited

Loading