User:Kbseah
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Hello world!
Queries
[edit]Example queries for taxa
[edit]- Labels and descriptions for ciliate classes
- Ciliate species without descriptions in Chinese
- Ciliate genera with the same taxon name (Find homonyms and duplicates)
- Ciliate genera with same taxon name as any other taxa (Find hemihomonyms)
- Ciliate families optionally with reference to first valid descriptions
- Works authored by Wilhelm Foissner where main subject is a taxon
- Eponymous ciliate taxa (list very incomplete)
- Filter ciliate taxa by regex on taxon author citation, optionally get existing taxon-author and year of publication qualifiers https://w.wiki/7HB4
- Ciliate species with French Wikipedia articles
- Ciliate genera without GBIF taxon ID
- Taxa not linked to reference with nomenclatural act but which have a Wikispecies page
- Retrieve all combinations of a given species (whether original combination or not)
- Retrieve 'taxon name' statements where reference is qualified with 'reference has role'
- Retrieve 'taxonomic type' statements where reference is qualified with 'reference has role'
- Articles published in the Journal of Eukaryotic Microbiology with "n. sp." in the title which are referenced in a taxon name statement with a specified role - uses the MWAPI to search labels
- Articles published in IJSEM with "n. sp." in the title with a taxon as a main subject
Use CirrusSearch for searches that would otherwise timeout with SPARQL, see.
Wrongly reconciled/conflated topics in "main subject" statements
[edit]- Articles in journals for fields protistology or phycology with main subject "colonialism" - probably mistakenly inferred from keyword "colonial" in the title
I think the wrongly reconciled main topic statements should be deprecated, rather than deleted. This is because they appear to be added by scripted edits. If they are deleted, then there is the possibility that they will simply be added again, but if deprecated, the script author may notice the edit conflict and change their search strategy accordingly.
- "colonial" in articles about biology wrongly reconciled with "colonialism". https://w.wiki/AdEN
- "dark matter" in articles about biology (buzzwords like "microbial dark matter") wrongly reconciled with "dark matter" (concept in physics). https://w.wiki/AdEK
To do
[edit]To be fixed
[edit]- Remove redundant "instance of taxon" statements from items that are already "instance of fossil taxon": https://w.wiki/B2uN
- whoops: https://www.wikidata.org/w/index.php?title=Q129930499&oldid=2237722799
- Bacterial taxa with names ending in "sp.": https://w.wiki/B32z Some of these appear to be created from BacDive records, where they refer to cultivated strains that have not been assigned to a named species, but the strain identifier has been stripped away. As a result, they have been linked to Genbank assembly accession numbers for potentially unrelated strains/species, as those assembly records are associated with an NCBI placeholder taxon, e.g. see Roseomonas sp. (Q29565246).
- Fix first valid publications wrongly linked because of homonyms: https://w.wiki/BBsi
- References for bacterial names published outside of International Journal of Systematic and Evolutionary Microbiology (Q3511931) or International Journal of Systematic Bacteriology (Q26827892) (except Cyanobacteria!) should not have role first valid description (Q1361864) but use effective publication (Q130297343) instead: https://w.wiki/BBz2
Fix titles of articles with scientific names wrongly processed
[edit]- Titles with scientific names that were erroneously removed. https://www.wikidata.org/w/index.php?title=Q60458631&oldid=1185683710
- Titles with scientific names not set off by spaces from surrounding words.
- The above appear to originate upstream from incorrect processing of titles in CrossRef and PubMed.
- Encoding issues in titles and name strings: https://www.wikidata.org/w/index.php?title=Q54802341&oldid=1833160994
A hierarchy of tasks
[edit]- Generate labels and descriptions from statements within an item
- Link items within Wikidata using statements/labels of the items
- Link items in Wikidata to external identifiers in databases that are programmatically accessible
- Add statements to Wikidata based on sources that are not programmatically accessible
Extract structured data semi-manually from published works
[edit]Link Kofoid & Campbell, 1929 taxa to A conspectus of the marine and fresh-water ciliata belonging to the suborder Tintinnoinea, with descriptions of new species principally from the Agassiz expedition to the eastern tropical Pacific 1904-1905 (Q122310402)- Genera of ciliates listed in Catalogue of the Generic Names of Ciliates (Q95986077)
- Protist taxa described by Saville-Kent, see Zoological Record
- Homonyms listed in Corliss 1960 The Problem of Homonyms among Generic Names of Ciliated Protozoa, with Proposal of Several New Names* (Q103867709)
- Genera of microsporidians listed in Checklist of Available Generic Names for Microsporidia with Type Species and Type Hosts (Q123498442)
- Replacement names in https://www.researchgate.net/publication/304370291_Replacement_names_for_botanical_taxa_involving_algal_genera and https://www.biotaxa.org/Phytotaxa/article/view/phytotaxa.268.2.7
- Replacement names in https://www.researchgate.net/publication/339551389_Monograph_Every_sponge_its_own_name_removing_Porifera_homonyms
Data cleaning and linking
[edit]- Link taxa to works where names first validly published
- Publications of bacterial taxa
- Find and disambiguate homonyms
- Add basic descriptions for taxa based on vernacular names of higher taxa (e.g. "species of green algae")
- Add vernacular names @zh for taxa from zhwiki sitelinks: use this query, have to figure out how to unescape the characters
- Link errata to the articles they correct by matching titles
- Link taxa to identifiers in GBIF, IRMNG, NCBI, etc., matching higher taxa to avoid homonyms: Use the Global Names reconciliation service?
- Link/create Wikidata items for reference templates in specieswiki; use Petscan to search
- Find items in Wikidata which (may) lack BHL part items/Biostor items. Query. Use Biostor reconciliation service to check if they are already in Biostor.
- User:Kbseah/How to model cryptic species?
Authors and basionyms for taxa of mosses
- Add taxon author citations to taxa of mosses moss (Q25347) sourced from World Flora Online data export
- Parse taxon author citation and match to botanist author abbreviations, to add taxon author and ex taxon author qualifiers (if not already present)
- Parse taxon author citation to find items that are recombinations but without basionym statements; add basionyms statements sourced from World Flora Online
- Explore parsing abbreviated citations from World Flora Online to match taxa to first valid descriptions or other nomenclatural acts
Data modeling questions
[edit]- How to qualify reference where role is type designation?
- How to represent taxon authors as qualifiers of taxon name statement if no item for author exists? (e.g. names we can't disambiguate)
- How to represent order of taxon authors as qualifiers of taxon name statement?
- Better to have nomenclatural acts, taxonomic treatments, etc. as objects of "described by" statements? Then these statements themselves can be qualified and ranked. For example, if the first valid description was found from a third party citation or if its status is disputed.
- How to deal with edits like this? https://www.wikidata.org/w/index.php?title=Q27197072&oldid=413236593
KIV
[edit]- World Foraminifera Database https://www.marinespecies.org/foraminifera/index.php
- Journal title abbreviations in Zool Record
- What caused this?! https://www.wikidata.org/w/index.php?title=Q18519822&diff=prev&oldid=1753573010
- Study this query
- wat: Spontaneous Female Orgasms Triggered by the Smell of a Newly Found Tropical Dictyophora Desv. Species (Q29011578)
- to be merged? or a homonym: Amanita gemmata (Q105049169)
- Should objects like this be merged? Chirogalus samati (Q122228399)
- The Online Books Page - useful for finding full texts
Scriptable tasks
[edit]- Replace Den "taxon" with more informative descriptions, e.g. "species of bacteria"
- Link bacterial taxa to LPSN pages
- Replace old bacterio.net LPSN links with the new domain
- From publications with Zoobank identifiers, get nomenclatural acts and link them on Wikidata
- Add qualifier "object of statement has role" "recombination" for taxon name statements if taxon item has "original combination" or "basionym" statements: https://qlever.cs.uni-freiburg.de/wikidata/vZAYcK
- Add reciprocal "taxon synonym of", "protonym of", "basionym of" statements or vice versa, and copy references if present