egonw

#defaultView:BarChart
SELECT ?year (count(distinct ?citing_work) as ?count) ?workLabel WITH {
  SELECT (count(distinct ?citing_work) as ?totalCount) ?work WHERE {
    ?work wdt:P50 / wdt:P496 "0000-0001-7542-0286" .
    ?citing_work wdt:P2860 ?work .
  } group by ?work
    order by DESC(?totalCount)
    limit 10
} AS %PAPERS WHERE {
  INCLUDE %PAPERS

egonw

# tool: scholia
#defaultView:Graph
PREFIX target: <http://www.wikidata.org/entity/Q211171>

SELECT ?class ?classLabel ?otherclass ?otherclassLabel ?rgb WITH {
  SELECT DISTINCT ?class ?otherclass ?rgb WHERE {
    { VALUES ?class_ { target: }
      { ?otherclass_ wdt:P279 ?class_ . BIND( "3182BD" AS ?rgb) BIND(?class_ AS ?class) BIND(?otherclass_ AS ?otherclass) }
      UNION
      { ?otherclass_ wdt:P31 ?class_ . BIND( "E6550D" AS ?rgb) BIND(?class_ AS ?class) BIND(?otherclass_ AS ?otherclass) }

egonw

SELECT (SUBSTR(STR(?wikidata),32) AS ?qid)
  (CONCAT("\"\"\"", ?inchikey_, "\"\"\"") AS ?inchikey)
  (CONCAT("\"\"\"", ?inchi_, "\"\"\"") AS ?inchi)
  (CONCAT("\"\"\"", ?chemform_, "\"\"\"") AS ?chemform)
  (CONCAT("\"\"\"", ?smiles_, "\"\"\"") AS ?smiles)
  (CONCAT(str(?mass_), "U483261") AS ?mass)
WHERE {
  VALUES ?inchikey_ { "WSYNAKWAAXYNMW-DEOSSOPVSA-N" "PTCHLTYDAIWNSD-SSDOTTSWSA-N" "GAZIIOYXDWTTMC-GFCCVEGCSA-N" "CIUYPOUJRYWLDF-QFIPXVFZSA-N" "HAGZRCCJXLGJTR-BDAKNGLRSA-N" }
  ?wikidata wdt:P235 ?inchikey_ ;
            wdt:P234 ?inchi_ ;

egonw

Project 26 notes BioHackathon Europe 22

Potentially interesting metabolomics datasets:

These datasets have been found in the Metabolights repository (annotated with ChEBI, (class)name, SMILES*, InChI*) and Metabolomics workbench(annotated with PubChem*, Kegg*), through the search term 'toxic' (the term 'UVCB' gave 0 results). *If available?

ID	Species	Chemical(s)	Comment(s)	Technique	Annotated IDs	Unannotated peaks
MTBLS275	mouse (Mus musculus)	chlorpyrifos; chlorpyrifos-methyl metabolite(3,5,6-trichloro-2-pyridinol)	oral exposure	NMR	52	2+?
MTBLS48	mouse (Mus musculus)	Municipal wastewater effluents (MWWE)	transcriptomic data also available	NMR	47	1+?

egonw

Conference Tooting Community Standard

Conference tooting is the Mastodon equivalent of tweeting at and about conferences, particularly scientific content of those meetings, where commonly a meeting conference hashtag is is used. This creates an online discussion sphere where the topic of the meeting can be discussed. Normally, participants of the meeting only use the hashtag.

Because the 'local timeline' of can get crowded quickyl, the Mastodon platform has various mechanisms to reduce the flood of that timeline, putting focus on seeds. This has implications how we tweet conferences. This Mastodon server expects the following behavior:

egonw

#defaultView:Map
PREFIX venue: <http://www.wikidata.org/entity/Q180445>
SELECT DISTINCT ?author ?geo

WITH {
SELECT DISTINCT ?author_ ?author WHERE {
  {
    ?target p:P50 ?author_statement ; wdt:P1433 venue: .
    ?author_statement ps:P50 ?author_ .
    ?author_ rdfs:label ?author .

egonw

Parsed CCCC\C=C/CCCCCCCC(=O)OC[C@@]([H])(O)COP([O-])(=O)OCC[N+](C)(C)C into CDKMolecule:C22H44NO7P
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
InChIKey match: http://www.wikidata.org/entity/Q27144114
====================
C₂₂H₄₄NO₇P is already in Wikidata as http://www.wikidata.org/entity/Q27144114
Full stereochemistry is defined
====================
Parsed [H][C@@](O)(COC(=O)CCCCCCCCCCCCCC)COP([O-])(=O)OCC[N+](C)(C)C into CDKMolecule:C23H48NO7P

egonw

# (C) 2019 Andra Waagmeester
#     2019 Egon Willighagen
#
# MIT License

from wikidataintegrator import wdi_core, wdi_login, wdi_helpers
import os
import sys

if "WDUSER" in os.environ and "WDPASS" in os.environ:

egonw

# tool: scholia
#defaultView:Table
PREFIX target: <http://www.wikidata.org/entity/Q7160367>

SELECT
  (MIN(?dates) AS ?date)
  ?work ?workLabel
  (GROUP_CONCAT(DISTINCT ?type_label; separator=", ") AS ?type)
  (GROUP_CONCAT(DISTINCT ?winner_label; separator=", ") AS ?winners)
WHERE {

egonw

Parsed C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O into CDKMolecule:C6HF11O2
InChIKey match: http://www.wikidata.org/entity/Q27156874
PubChem CID match: http://www.wikidata.org/entity/Q27156874
====================
C₆HF₁₁O₂ is already in Wikidata as http://www.wikidata.org/entity/Q27156874
Full stereochemistry is defined
====================
Parsed C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O into CDKMolecule:C7HF13O2
InChIKey match: http://www.wikidata.org/entity/Q27116513
PubChem CID match: http://www.wikidata.org/entity/Q27116513