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Jtuom

Joined 27 January 2016
Babel user information
fi-N Tämän käyttäjän äidinkieli on suomi.
en-3 This user has advanced knowledge of English.
sv-2 Den här användaren har medelgoda kunskaper i svenska.
fr-1 Cet utilisateur dispose de connaissances de base en français.
de-1 Dieser Benutzer beherrscht Deutsch auf grundlegendem Niveau.
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Jouni T. Tuomisto
chief researcher
National Institute for Health and Welfare (THL)
Finland

  • Special interests: environmental health, decision support, open data.
  • Publication list

Global disease burden data from IHME instituteEdit

Description of data import was moved to User:John Cummings/Dataimporthub#Global disease burden data from IHME institute. The last version on this page is archived.

A permanent link to IHME data: global disease burden (DALYs and deaths for 2016) [1]

Original data described and preprocessed in Opoasnet.

Remember also these: Years of potential life lost (Q2852035), number of injured (P1339), number of missing (P1446), number of casualties (P1590), mortality in Finland (Q24175139)

See instructions on Wikidata:Data Import Guide and User:John Cummings/Dataimporthub. For SPARQL Wikidata:SPARQL tutorial.

Example query in SPARQL (finds 1048 rows but with poor sensitivity and specificity):

The following query uses these:

  • Properties: instance of (P31)    , subclass of (P279)    , ICD-10 (P494)    
     1 PREFIX schema: <http://schema.org/>
     2 
     3 SELECT ?disease ?diseaseLabel (MIN(?icd) AS ?ICD10) ?article WHERE {
     4   ?disease wdt:P31/wdt:P279* wd:Q12136.
     5   ?disease wdt:P494 ?icd.
     6   ?article schema:about ?disease.
     7   ?article schema:isPartOf <https://en.wikipedia.org/>.
     8   SERVICE wikibase:label { bd:serviceParam wikibase:language "en,[AUTO_LANGUAGE]". }
     9 }
    10 GROUP BY ?disease ?diseaseLabel ?article
    11 ORDER BY ?diseaseLabel
    12 LIMIT 2000
    

Template: Medical propertiesEdit

Opasnet - Wikidata connectionEdit

We start the pilot by adding some existing disease burden data from a credible source (IHME Institute) into Wikidata and link to those data from Wikipedia.

The first set of data that is to be uploaded to Wikidata is the burden of disease estimates. Global estimates from the IHME Institute to English Wikipedia to populate disease and risk factor pages. For details of this work, see Burden of disease.

When adding data to Wikidata, there are some tricks you should know. These can be found from the documentation as well, but I highlight some issues that may save time and trouble.

Items and propertiesEdit

Properties are things that define the relation of the item and the value. Technically, items and properties are wiki pages in Wikidata and they have a unique number starting with Q (items) or P (properties). A particular property only accepts certain kind of values. Often values are also items, but sometimes numbers or strings.

See 'Help:Modeling causes' for examples and discussion.

For diseases, use has contributing factor rather than has cause when linking risk factors, because almost always a disease has several risk factors, and often one risk factor works with others to cause a case. Also, even if a risk factor is the single cause of a particular case, we do not want to imply that ALL cases of that disease are caused by a single risk factor.

All statements should have references. References are also statement triplets within a main statement. This kind of references should be used, in the order of preference. For details, see Help:Sources.

  • inventory number (P217) for URN numbers (URN itself is not a property!?)
  • Stated in (P248) requires an item as the value. So, if you want to have e.g. a book as reference, you must first add the book as item to the database and then link to the item. See Help:Sources before doing this.
  • Reference URL (P854) is the default property for some reason. However, use it only if the reference already has been added to Wikidata as item.
  • Imported from (P143) should be used if the data comes directly from another database. This is relevant if/when Opasnet (or part of it) is considered as a credible source and data can be directly downloaded from there.
    • For example: Imported from (P143) Opasnet (Q7095608)

Also organisations can be used as references:

  • imported from (P143) National Institute for Health and Welfare (Q4354957)
    • Institute for Health Metrics and Evaluation (Q6039400)
  • Opasnet (Q7095608) in Wikidata

Other useful:

We need a properties and units of measurement. This is how it goes.

Environmental and other pages where we might want to add infoboxes:


Other things

Examples

lead (Q708) → "exposure" 0.5 umol/l

criterion used (P1013) blood concentration (Q24276435)
location (P276) India (Q668)
of (P642) child (Q7569)
point in time (P585) 2014

Useful propertiesEdit

Wikidata properties and lists of properties
By number 0–99 · 100–199 · 200–299 · 300–399 · 400–499 · 500–599 · 600–699 · 700–799 · 800–899 · 900–999 · 1000–1099 · 1100–1199 · 1200–1299 · 1300–1399 · 1400–1499 · 1500–1599 · 1600–1699 · 1700–1799 · 1800–1899 · 1900–1999 · 2000–2099 · 2100–2199 · 2200–2299 · 2300–2399 · 2400–2499 · 2500–2599 · 2600–2699 · 2700–2799 · 2800–2899 · 2900–2999 · 3000–3099 · 3100–3199 · 3200–3299 · 3300–3399 · 3400–3499 · 3500–3599 · 3600–3699 · 3700–3799 · 3800–3899 · 3900–3999 · 4000–4099 · 4100–4199 · 4200–4299 · 4300–4399 · 4400–4499 · 4500–4599 · 4600–4699
Other Property proposals (index) · Constraint violations · Special real-time list · Real-time list by datatype · Database report


Sets and logicalEdit

property does not exist. Use "id=new" if it's to be created.

ArgumentationEdit

Title ID Data type Description Examples Inverse
instance ofP31Iteminstance of: that class of which this subject is a particular example and member (subject typically an individual member with a proper name label); different from P279; using this property as a qualifier is deprecated—use P2868 or P3831 insteadNelson Mandela <instance of> human-
subclass ofP279Itemsubclass of: all instances of these items are instances of those items; this item is a class (subset) of that item. Not to be confused with P31 (instance of)apple <subclass of> fruit-
is a list ofP360Itemcommon element between all listed itemslist of Presidents of France <is a list of> humanhas list
part ofP361Itempart: object of which the subject is a part (it's not useful to link objects which are themselves parts of other objects already listed as parts of the subject). Inverse property of "has part" (P527, see also "has parts of the class" (P2670)).ear <part of> headhas part
said to be the same asP460Itemsynonym and Wikimedia duplicated page: this item is said to be the same as that item, but the statement is disputedMaidilibala <said to be the same as> Uskhal Khan Tögüs Temür-
opposite ofP461Itemopposite and antonym: item that is the opposite of this itemblack <opposite of> white-
has partP527Itemhas part, consist of and meronymy: part of this subject; inverse property of "part of" (P361). See also "has parts of the class" (P2670).Eurasia <has part> Europe and Asiapart of
used byP1535Itemuser: item or concept that makes use of the subject (use sub-properties when appropriate)remote control unit <used by> TV-watcheruses
usesP2283Itemuse: item or concept used by the subject or in the operation (see also instrument [P1303] and armament [P520])painter <uses> paint brushused by
has qualityP1552Itemquality: the entity has an inherent or distinguishing non-material characteristichuman <has quality> genderof
manifestation ofP1557Itemmanifestation: inherent and characteristic embodiment of a given conceptorganism <manifestation of> life-
subproperty ofP1647Propertyall resources related by this property are also related by that propertyparent taxon <subproperty of> subclass of-
inverse propertyP1696Propertyinverse: links a property to its inverse propertypart of <inverse property> has part-
equivalent classP1709URLequivalence class: equivalent class in other ontologies (use property URI)bus stop <equivalent class> https://schema.org/BusStop-
input setP1851Iteminput set: a superset of the domain of a function or relation that may include some inputs for which the function is not defined; to specify the set of only those inputs for which the function is defined use domain (P1568)tangent <input set> set of real numbers-
different fromP1889Itemdifference: item that is different from another item, with which it is often confusedKowalski <different from> Kowalski-
properties for this typeP1963Propertywhen this subject is used as object of "instance of" or "occupation", the following properties normally applyscientist <properties for this type> educated at-
classification of raceP2502Itemrace for which this classification appliesgeneral classification of the 2015 Coupe Sels <classification of race> 2015 Schaal Selsresults
statement is subject ofP805Item(qualifier only) item which describes the relation identified in this statementBarack Obama <statement is subject of> presidency of Barack Obama-

CausalitiesEdit

Title ID Data type Description Examples Inverse
approved byP790Itemitem is approved by other item(s) [qualifier: statement is approved by other item(s)]GNU General Public License <approved by> Open Source Initiative-
statement disputed byP1310Itementity that disputes a given statementWaltz No. 17 in E-flat major, Op. posth. <statement disputed by> Chomiński catalog-

Health-relatedEdit

Title ID Data type Description Examples Inverse
has causeP828Itemcause: underlying cause, thing that ultimately resulted in this effectmercury poisoning <has cause> mercuryhas effect
has immediate causeP1478Itemcause: nearest, proximate thing that directly resulted in the subject as outcome or effect. Used in conjunction with 'has cause' (i.e. underlying cause) and 'has contributing factor'. See 'Help:Modeling causes'.Cretaceous–Paleogene extinction event <has immediate cause> starvation and impact winterimmediate cause of
has contributing factorP1479Itemcontributing factor: thing that significantly influenced, but did not directly cause, this outcome or effect. Used in conjunction with 'has cause' and 'has immediate cause'. See 'Help:Modeling causes'.American Civil War <has contributing factor> caning of Charles Sumnercontributing factor of
immediate cause ofP1536Itemcause: immediate cause of this effectAmerican Civil War <immediate cause of> assassination of Abraham Lincolnhas immediate cause
contributing factor ofP1537Itemthing that is significantly influenced by this cause, but does not directly result from it. See 'Help:Modeling causes' for examples and discussion.obesity <contributing factor of> heart diseasehas contributing factor
has effectP1542Itemeffect and cause: effect of this causemercury <has effect> mercury poisoninghas cause

ReferencesEdit

These properties are in the order of preference. Stated in is used for references that are Wikidata items.

Title ID Data type Description Examples Inverse
route of administrationP636Itemroute of administration: path by which a drug, fluid, poison, or other substance is taken into the bodyaspirin <route of administration> intramuscular injection-
symptomsP780Itemsymptom: possible symptoms of a medical conditionmeningitis <symptoms> headache-
pathogen transmission processP1060Itempathogen transmission: process by which a pathogen is transmitted, equivalent to "transmitted by" in the relation ontology http://purl.obolibrary.org/obo/RO_0002451influenza <pathogen transmission process> airborne transmission-
populationP1082Quantitypopulation size: number of people inhabiting the place; number of people of subjectSan Francisco <population> 892,533-
prevalenceP1193Quantityprevalence: portion of a population with a given diseaseHuntington disease <prevalence> 0.000123-
manner of deathP1196Itemmanner of death: general circumstances of a person's death; e.g. natural causes, accident, suicide, homicide, pending investigation or special 'unknown value'. Use 'cause of death' (P509) for more immediate or underlying causes, e.g. heart attack, car accidentAdolf Eichmann <manner of death> capital punishment-
number of injuredP1339Quantityinjury: number of people with non-fatal injuries in an eventSeptember 11 attacks <number of injured> 6,000-
number of missingP1446Quantitynumber of people missing after an event - qualify with "point in time (P585)"2013 Lushan earthquake <number of missing> 23-
number of survivorsP1561Quantitynumber of people surviving an eventEssing bridge accident <number of survivors> 1-
number of casualtiesP1590Quantitynumber of people dead or injured because of this event. Used when precise data on number of deaths and number of injured is unavailable.Hurricane Patricia <number of casualties> 8-
number of casesP1603Quantitynumber of cases: cumulative number of confirmed, probable and suspected occurrencesEbola virus epidemic in West Africa <number of cases> 13,703-
side effectP1909Itemside effect and adverse drug reaction: effect of a medication or procedure, that occurs next to the desired effectInfluenza vaccine <side effect> sore throat-
half-lifeP2114Quantityhalf-life: time required for the amount of something to fall to half its initial valueuranium-235 <half-life> 704,000,000 annum-
life expectancyP2250Quantitylife expectancy: life expectancy for this group or speciesPug <life expectancy> 13.5 year-
time period of periodically occurring eventP2257Quantityrecurring: standard nominal interval between scheduled or regularly recurring events. Include unit of time, e.g. "year" (Q577)Olympic Games <time period of periodically occurring event>year-
minimal lethal doseP2300Quantitylowest published lethal dose: lowest concentration of a toxic substance in an environmental medium that kills individual organisms or test species under a defined set of conditionsacetone <minimal lethal dose> 45.455 parts per million-
incidenceP2844Quantityincidence: probability of occurrence of a given condition in a population within a specified period of timehepatitis C <incidence> 0.5 cases per 100000 person-years-
disease burdenP2854Quantitydisease burden: impact of a health problem as measured by financial cost, mortality, morbidity, or other indicators. It is often quantified in terms of quality-adjusted life years (QALYs) or disability-adjusted life years (DALYs)tuberculosis <disease burden> 34,200,000 disability-adjusted life year-

Property constraintsEdit

Title ID Data type Description Examples Inverse
stated inP248Itemto be used in the references field to refer to the information document or database in which a claim is made; for qualifiers use P805Property talk:P248-
PubMed IDP698External identifierPubMed ID: identifier for journal articles/abstracts in PubMedEvolution in Mendelian Populations <PubMed ID> 17246615-
DOIP356External identifierdigital object identifier: serial code used to uniquely identify digital objects like academic papersEcological guild evolution and the discovery of the world's smallest vertebrate. <DOI> 10.1371/JOURNAL.PONE.0029797-
inventory numberP217Stringitem of collection or exhibition: identifier for a physical object or a set of physical objects in a collectionThe Night Watch <inventory number> SK-C-5-
reference URLP854URLUniform Resource Locator: should be used for internet URLs as references. Use P4656 for interwiki linksJames Barry <reference URL> http://www.newscientist.com/article/mg19726462.000-histories-the-male-military-surgeon-who-wasnt.html-
imported from Wikimedia projectP143Itemsource of this claim's value; used in references section by bots importing data from Wikimedia projects; also allowed to be used for manual importsProperty talk:P143-
PubMed HealthP653External identifierPubMed: identifier for a physiological condition, in the PubMed Health websitemyocardial infarction <PubMed Health> PMH0001246-
see alsoP1659Propertyused to indicate another property that might provide additional information about the Wikidata-propertywebsite account on <see also> Twitter username and Facebook ID-

OtherEdit

Title ID Data type Description Examples Inverse
property constraintP2302Itemproperty constraint: constraint applicable to this Wikidata propertyIMDb ID <property constraint> distinct values constraint-
exception to constraintP2303Itemitem that is an exception to the constraint, qualifier to define a property constraint in combination with P2302Property talk:P2303-
group byP2304PropertyGROUP BY: qualifier to define a property constraint in combination with P2302 (Wikidata property constraint)Property talk:P2304-
item of property constraintP2305Itemqualifier to define a property constraint in combination with P2302Property talk:P2305-
propertyP2306PropertyWikidata property: qualifier to define a property constraint in combination with P2302 (property constraint), or to limit the scope of Q44292881 (wikidata statement)Property talk:P2306-
namespaceP2307StringHelp:MediaWiki namespace: qualifier to define a property constraint in combination with P2302 (Wikidata property constraint)Property talk:P2307-
classP2308Itemclass (set theory): qualifier to define a property constraint in combination with P2302Property talk:P2308-
relationP2309Itemrelation and relation: qualifier to define a property constraint in combination with P2302. Possibly values are: "instance of", "subclass of" or "instance or subclass of". The qualifier to use with the property "relative" is "type of kinship" (P1039), not this.Property talk:P2309-
minimum date (property constraint)P2310Point in timequalifier to define a property constraint in combination with P2302Property talk:P2310-
maximum date (property constraint)P2311Point in timequalifier to define a property constraint in combination with P2302. Use "unknown value" for current date.Property talk:P2311-
maximum valueP2312Quantitymaximum: qualifier to define a property constraint in combination with P2302. "no value" can be used to specify no upper boundrange constraint-
minimum valueP2313Quantityminimum: qualifier to define a property constraint in combination with P2302range constraint-
comment (DEPRECATED)P2315Monolingual textto be deleted: replace with "syntax clarification" (P2916) or add the usage note in the items description.Property talk:P2315-
constraint statusP2316Itemqualifier to define a property constraint in combination with P2302. Use values "mandatory constraint" or "suggestion constraint"property scope constraint <constraint status> mandatory constraint-

property does not exist. Use "id=new" if it's to be created.

property does not exist. Use "id=new" if it's to be created. property does not exist. Use "id=new" if it's to be created. property does not exist. Use "id=new" if it's to be created. property does not exist. Use "id=new" if it's to be created.

Title ID Data type Description Examples Inverse
followsP155Itemfollows: immediately prior item in a series of which the subject is a part [if the subject has replaced the preceding item, e.g. political offices, use "replaces" (P1365)]Star Wars Episode V: The Empire Strikes Back <follows> Star Wars Episode IV: A New Hopefollowed by
followed byP156Itemfollowed by: immediately following item in a series of which the subject is a part [if the subject has been replaced, e.g. political offices, use "replaced by" (P1366)]Star Wars Episode IV: A New Hope <followed by> Star Wars Episode V: The Empire Strikes Backfollows
applies to partP518Itempart, aspect, or form of the item to which the claim appliesLady with an Ermine <applies to part> painting surface-
start timeP580Point in timestart time: time an item begins to exist or a statement starts being validJapan <start time> -
end timeP582Point in timeend time: time an item ceases to exist or a statement stops being validBaroque <end time> 1750s
date QS:P,+1750-00-00T00:00:00Z/8
-
point in timeP585Point in timepoint in time: time and date something took place, existed or a statement was trueMalaysia Airlines Flight 17 <point in time> -
ofP642Itemqualifier stating that a statement applies within the scope of a particular itemJean-Baptiste Le Moyne de Martigny <of> Rochefourchathas quality
cause of destructionP770Itemcause of destruction: item which caused the destruction of the subject itemColossus of Rhodes <cause of destruction> earthquakedestroyed
separated fromP807Itemsubject was founded or started by separating from identified objectPresbyterian Church in America <separated from> Presbyterian Church in the United States-
excludingP1011Itemusually used as a qualifierBritish Islands <excluding> Ireland-
includingP1012Itemusually used as a qualifier2015 San Bernardino shooting <including> suspect-
criterion usedP1013Itemcriterion: property by which a distinction or classification is mademale <criterion used> gender binary and population <criterion used> population without double counting-
product or material producedP1056Itemproduct: material or product produced by a government agency, business, industry, facility, or processJaduguda Uranium Mine <product or material produced> uraniummanufacturer
proportionP1107Quantityproportion: to be used as a qualifier, value must be between 0 and 1mayonnaise <proportion> 0.7-
quantityP1114Quantitynumber of objects: number of instances of this subjectstate of the United States <quantity> 50-
valid in periodP1264Itemtime period when a statement is validTübingen <valid in period> standard time-
facet ofP1269Itemtopic of which this item is an aspect, item that offers a broader perspective on the same topicwater (data page) <facet of> water-
rankingP1352Quantitythe subject's numbered position within a competition or group of performersXu Xin <ranking> 2,014-
replacesP1365Itemreplaced object: person or item replaced. Use P1398 (structure replaces) for structures. Use P155 (follows) if the previous item was not replaced or if predecessor and successor are identicalBarack Obama <replaces> George W. Bushreplaced by
replaced byP1366Itemreplacing subject: other person or item which continues the item by replacing it in its role. Use P156 (followed by) if the item is not replaced (e.g. books in a series), nor identical, but adds to the series without dropping the role of this item in that seriesPtolemy XII Auletes <replaced by> Cleopatrareplaces
domainP1568Itemdomain of a function: set of "input" or argument values for which a mathematical function is definedsquare function <domain> real number-
Wikidata propertyP1687PropertyWikidata property: main Wikidata property for this itemacademic discipline <Wikidata property> studied bysubject item of this property
measured byP1880Itemscale by which a phenomenon is measuredearthquake <measured by> Richter scale-
relative toP2210Itemreference point: qualifier: what a statement value is relative toProperty talk:P2210-
intended publicP2360Itemtarget audience: this work, product, object or event is intended for, or has been designed to that person or group of people, animals, plants, etcNaive Set Theory <intended public> teenager-
resultsP2501Itemresults of a competition in sports2015 Schaal Sels <results> general classification of the 2015 Coupe Selsclassification of race