User:Charles Matthews/ContentMine workshop 3 March 2019

Links

• NCBI2wikidata and GMT tools on GitHub
• ScienceSourceIngest tool on GitHub
• PubMed - Searching Medical Literature: Using Medical Subject Headings (MeSH)
• WD:SSFL for the focus list
• ScienceSource wiki is at http://sciencesource.wmflabs.org
• SS data schema
• List of articles on the ScienceSource wiki
• ScienceSource pulmonology drugs found
• Display of drugs and diseases in Nosocomial Legionnaire's disease--a case report and review of the literature (Q35653011), including cephalothin (Q2736126), erythromycin (Q213511) and tobramycin (Q1758380)
• http://sciencesource.wmflabs.org/wiki/Article:Nosocomial_Legionnaire%27s_disease--a_case_report_and_review_of_the_literature_(4532100)
• Another such display
• w:WP:MEDRS
• See here for the first version of a MEDRS algorithm, and below for a possible handling of MEDDATE for neglected diseases.
• Directory of Open Access Journals (DOAJ). Algorithm output depends on adding the DOAJ ID: missing information issue.

Endocrinology diseases

#Instance of disease, medical speciality pulmonology
SELECT ?item ?itemLabel
  WHERE {
  ?item wdt:P31 wd:Q12136 .
  ?item wdt:P1995 wd:Q203337 .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en" }
}

Try it!

PLOS list subjects query

Comment: Run without DOAJ and add info on journals ...

SELECT DISTINCT ?item ?itemLabel ?journalLabel ?subjectLabel

  WHERE {
  
    ?item wdt:P5008 wd:Q55439927;
          wdt:P31 wd:Q7318358;
          wdt:P577 ?date;
          wdt:P1433 ?journal.
         ?journal wdt:P5115 [ ].
        {VALUES ?subject 
        {wd:Q949694 wd:Q2447562 wd:Q649558 wd:Q326071 wd:Q203133
                  wd:Q842428 wd:Q11679861 wd:Q2264130 wd:Q2360849 wd:Q1345113
                  wd:Q1597571 wd:Q2841329 wd:Q2665559 wd:Q30953 wd:Q738292
                  wd:Q154874 wd:Q2859732 wd:Q39222 wd:Q326638 wd:Q162272
                  wd:Q809561 wd:Q18975737 wd:Q1017169 wd:Q12090 wd:Q327298
                  wd:Q326648 wd:Q18975220 wd:Q36956 wd:Q155098 wd:Q690032
                  wd:Q193216 wd:Q682798 wd:Q922029 wd:Q41083 wd:Q76973
                  wd:Q16877704 wd:Q247096 wd:Q167178 wd:Q304601
                  wd:Q331283 wd:Q1475667 wd:Q388646 wd:Q777087 wd:Q1102300
                  wd:Q1048084 wd:Q719656 wd:Q2528129 wd:Q1760607 wd:Q192100
                  wd:Q1137321 wd:Q221159
                 } 
        }      
      ?item wdt:P921 ?subject.

    FILTER (?date >= "2011-01-01T00:00:00Z"^^xsd:dateTime)
 
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
    }

Try it!