To Curate

SPARQL queries and material to curate

This note lists the remaining query bundles and scratch materials that still need curation before they can be added to the cleaned query index.

For each item below:

Decide the endpoint first: Wikidata Query Service, Qlever Wikidata, Qlever Metrin KG, IDSM/Sachem, or other.
Give the query a stable title in sentence case.
Write a one-line description that states the input, the filter, and the main output.
Keep the short query link if one exists. Remove raw embedded ?query= URLs from the curated note unless the full text must be preserved.
Record whether the item is a query, query family, endpoint note, draft SPARQL block, or presentation/scratch material.
Deduplicate variants. If multiple links differ only by output format or a small filter, keep one parent title and list the variants under it.
If the item is still exploratory or broken, keep it in this note and add a short reason.

Sachem non-permanent endpoint note Source material: https://idsm.elixir-czech.cz:2443/sachem/#/search. Curation instruction: keep only if the endpoint is still relevant as a manual search tool; otherwise move it to a tools/endpoints note instead of the query index.
Sachem grand parents Source material: https://w.wiki/32Wz. Curation instruction: determine whether this is a structure-search query, a taxonomic summarisation query, or both; rename accordingly and note required inputs.

Unnamed LOTUS query family Source material: https://w.wiki/$Q$, https://w.wiki/$R3, https://w.wiki/$RD, https://w.wiki/$RR, https://w.wiki/$RU, and https://w.wiki/$SF. Curation instruction: open each link, identify what changes between the variants, group them under one parent title if they are the same query family, and keep only the variants that add a distinct result view or filter.

Quest / Daniel Mietchen prototype family Source material: https://w.wiki/5a7K, https://w.wiki/5a8b, https://w.wiki/5a8g, https://w.wiki/5a8t, https://w.wiki/5a9B, https://w.wiki/5a9T, and https://w.wiki/5a9g, plus the raw SPARQL blocks in wikidata.sparql.md. Curation instruction: split this family into clearly named subgroups such as main-subject curation, QuickStatements generation, and taxon-compound literature matching; mark which variants are working, experimental, or superseded.
Not working / no results prototypes Source material: the quest query mod from Mietchen to compounds (not working) and No error but no results neither blocks in wikidata.sparql.md. Curation instruction: do not add these to the cleaned query list yet; instead summarise why they fail, what was tried, and which working variant replaced them.
Curating query Source material: the raw SPARQL block under Curating query and links https://w.wiki/5a9T and https://w.wiki/5a9g. Curation instruction: title it based on outcome rather than process, for example by the property being curated (P703 / main subject), and keep the QuickStatements output behaviour explicit in the description.

Wikidata scholarly article split reminders Source material: https://w.wiki/Eexo, https://w.wiki/Eexs, https://w.wiki/Eext, and https://w.wiki/Eexz, plus the discussion excerpt in wikidata.sparql.md. Curation instruction: rewrite this as a short reference note explaining the graph split, when to use Qlever instead of WDQS, and which example query demonstrates the fix.

Embedded query.wikidata.org URLs Source material: long query.wikidata.org/index.html#... and query.wikidata.org/embed.html#... URLs in wikidata.sparql.md. Curation instruction: replace each embedded URL with a short title and, if possible, a w.wiki short link; keep the embedded form only in a dedicated archive note if the exact serialized query text matters.
Embedded qlever ?query= URLs Source material: long https://qlever.../?query=... URLs in the Qlever section of wikidata.sparql.md. Curation instruction: keep the stable short Qlever permalink as the curated link; archive the expanded URL only when it contains annotations or a version not represented by the short permalink.

Drug-protein interaction draft Source material: inline SPARQL block under ## drug-prot interaction. Curation instruction: convert this into a titled query entry only after confirming scope, expected output columns, and whether the cancer restriction is intentional or example-only.
VIT / JLW federated query blocks Source material: the two raw SPARQL blocks joining Wikidata with sinergiawolfender.org namespaces in wikidata.sparql.md. Curation instruction: decide whether these belong in a separate federated-query note; if kept, document the external dataset dependency, required taxon input, and matching logic on molecular formula.
InChIKey occurrence lookup drafts Source material: the containing taxa + ref for a given IK section with two raw SPARQL blocks and embedded URLs. Curation instruction: merge duplicate variants, name them by purpose (all taxa for an InChIKey prefix, taxon-restricted InChIKey lookup), and keep only one canonical version per use case.

Endpoint inventory Source material: https://www.wikidata.org/wiki/Wikidata:Lists/SPARQL_endpoints. Curation instruction: move this out of the query index unless it is needed as a reference note; it is endpoint documentation rather than a query.

To tweet Source material: the # to tweet section in wikidata.sparql.md. Curation instruction: harvest any actual useful query links from the section and merge them into stable query families; discard the presentation framing.
Presentation example: UniFr Source material: # example for prsenattion UniFr with links https://w.wiki/4EMf and https://w.wiki/4EMo. Curation instruction: keep the underlying queries only if they are not already covered by an existing curated family; otherwise remove the presentation-specific label.
Manager Source material: the standalone Manager marker in wikidata.sparql.md. Curation instruction: remove unless it refers to a recoverable query context elsewhere in the source note.
mail_jakub Source material: [[mail_jakub|scratch.2021.02.02.150258.mail_jakub]]. Curation instruction: treat this as provenance for the indole-substructure idea, not as a query entry; move citation context to a note if useful.

Use this template when promoting an item into the cleaned note:

Title: one-sentence description. Query: <short link>. Variant: <second link if genuinely distinct>.

If a full SPARQL block must be preserved:

Create a dedicated note for the block.
Give it the same stable title.
In the cleaned index, link only the short query URL and mention that the full SPARQL is archived separately.