Jtuom
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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 institute Edit
- 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:
- Items: disease (Q12136)
- Properties: instance of (P31) , subclass of (P279) , ICD-10 (P494)
PREFIX schema: <http://schema.org/> SELECT ?disease ?diseaseLabel (MIN(?icd) AS ?ICD10) ?article WHERE { ?disease wdt:P31/wdt:P279* wd:Q12136. ?disease wdt:P494 ?icd. ?article schema:about ?disease. ?article schema:isPartOf <https://en.wikipedia.org/>. SERVICE wikibase:label { bd:serviceParam wikibase:language "en,[AUTO_LANGUAGE]". } } GROUP BY ?disease ?diseaseLabel ?article ORDER BY ?diseaseLabel LIMIT 2000
Template: Medical properties Edit
Opasnet - Wikidata connection Edit
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 properties Edit
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.
- We probably should add URL items such as Burden of disease (for global numbers) and Burden of disease in Finland].
- 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:
- Wikidata:Userboxes to identify oneself in Wikidata. Babel box is useful, because then Wikidata offers languages you actually know.
- Wikidata:WikiProject Medicine
- en:Module:Wikidata
- en:Template:Wikidata value
- Wikidata:Notes/Inclusion syntax
- mw:Wikidata Toolkit
We need a properties and units of measurement. This is how it goes.
- Incidence and disease burden have been suggested as properties, and I hope they are accepted. incidence (P2844) disease burden (P2854)
- Life expectancy already exists as a property life expectancy (P2250). The unit year (Q577) is attached to it. See also en:Life expectancy
- Applies to part applies to part (P518) property should be used for distinguishing subgroups such as sex, age etc. but only if the subject item is a population.
- Point in time point in time (P585) property should be used to distinguish the year of observation.
- Does item person-year exist so that it can be used in units such as DALY / 100000 person-years? Or does it need to be a property? Use metre metre (Q11573) as an example about what properties a unit item should have.
- Other relevant properties:
- en:Disease burden Wikipedia article
- tuberculosis tuberculosis (Q12204) example of a well-developed disease item. en:Tuberculosis has an infobox example
- Wikidata property for places Wikidata property related to places (Q19829914) Wikidata property for describing places. Might be useful to characterise things in e.g. building model.
- knowledge crystal result (Q23893445)
- Disease burden of air pollution (Q23680551)
- based on (P144) is used when you refer to several articles that were summarised in a knowledge crystal
- stated in (P248) is used when you refer to a knowledge crystal or article that is within Wikidata, e.g. Lelieveld 2015 The contribution of outdoor air pollution sources to premature mortality on a global scale (Q23670156)
- Global Burden of Disease (Q499419)
- disease burden (Q5282120)
- blood concentration (Q24276435) for e.g. exposure estimates
- years of potential life lost (Q2852035),
- number of injured (P1339), number of missing (P1446), number of casualties (P1590)
- mortality in Finland (Q24175139)
Environmental and other pages where we might want to add infoboxes:
- en:Dioxins and dioxin-like compounds
- en:Disability-adjusted life year
- en:Help:Infobox
- en:Study 329 example of a study with an infobox
- en:Template:Infobox drug
- en:Template:Infobox medical condition
- en:Template:Infobox medical intervention maybe not relevant for public health?
- en:Template:Infobox pandemic not much used but might be interesting to ROKO
- en:Template:Infobox nutritional value might be interesting for RAVY
- sotkanet these indicators might link to DALY estimates or calculations [2]
Other things
- en:Wikipedia:Meetup/NYC/Wikipedia Day 2016
- en:File:Wikipeda Day 15 (2016) NYC Wikidata.pdf
- Interface for making SPARQL queries to Wikidata
- Units of measurement:
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 properties Edit
By number |
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Other |
Sets and logical Edit
property does not exist. Use "id=new" if it's to be created.
Argumentation Edit
Title | ID | Data type | Description | Examples | Inverse |
---|---|---|---|---|---|
instance of | P31 | Item | instance of: that class of which this subject is a particular example and member; different from P279 (subclass of); for example: K2 is an instance of mountain; volcano is a subclass of mountain (and an instance of volcanic landform) | Nelson Mandela <instance of> human | - |
subclass of | P279 | Item | subclass of: this item is a subclass (subset) of that item; all instances of this item are instances of that item; different from P31 (instance of), e.g.: K2 is an instance of mountain; volcano is a subclass of mountain (and an instance of volcanic landform) | apple <subclass of> fruit | - |
is a list of | P360 | Item | list: common element between all listed items | list of presidents of France <is a list of> human | has list |
part of | P361 | Item | part: object of which the subject is a part (if this subject is already part of object A which is a part of object B, then please only make the subject part of object A), inverse property of "has part" (P527, see also "has parts of the class" (P2670)) | ear <part of> head | has part(s) |
said to be the same as | P460 | Item | said to be the same as: this item is said to be the same as that item, though this may be uncertain or disputed | Maidilibala <said to be the same as> Uskhal Khan Tögüs Temür | - |
opposite of | P461 | Item | opposite and antonym: item that is in some way the opposite of this item | war <opposite of> peace | opposite of |
has part(s) | P527 | Item | has part, consist of and meronymy: part of this subject; inverse property of "part of" (P361). See also "has parts of the class" (P2670). | United States Congress <has part(s)> United States Senate | part of |
used by | P1535 | Item | user: item or concept that makes use of the subject (use sub-properties when appropriate) | remote control <used by> television watcher | uses |
uses | P2283 | Item | use: item or concept used by the subject or in the operation (see also instrument [P1303] and armament [P520]) | painter <uses> paintbrush and paint | used by |
has quality | P1552 | Item | quality: the entity has an inherent or distinguishing non-material characteristic. use a more-specific property when possible | human <has quality> gender | of |
manifestation of | P1557 | Item | manifestation: inherent and characteristic embodiment of a given concept | organism <manifestation of> life | - |
subproperty of | P1647 | Property | subproperty: all resources related by this property are also related by that property | parent taxon <subproperty of> subclass of | - |
inverse property | P1696 | Property | inverse: links a property to its inverse property (which relates the subject and object in reverse order) | part of <inverse property> has part(s) | - |
equivalent class | P1709 | URL | equivalence class: equivalent class in other ontologies (use property URI) | bus stop <equivalent class> https://schema.org/BusStop | - |
input set | P1851 | Item | input 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 from | P1889 | Item | different from: item that is different from another item, with which it may be confused | Kowalski <different from> Kowalski | different from |
properties for this type | P1963 | Property | when this subject is used as object of "instance of", the following properties normally apply | bridge <properties for this type> number of spans and longest span | - |
classification of race | P2502 | Item | race for which this classification applies | general classification of the 2015 Coupe Sels <classification of race> 2015 Schaal Sels | results |
statement is subject of | P805 | Item | (qualifying) item that describes the relation identified in this statement | Barack Obama <statement is subject of> presidency of Barack Obama | - |
Causalities Edit
Title | ID | Data type | Description | Examples | Inverse |
---|---|---|---|---|---|
approved by | P790 | Item | guideline: item 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 by | P1310 | Item | controversy and opinion: entity that disputes a given statement | Waltz No. 17 in E-flat major, Op. posth. <statement disputed by> Chomiński catalog | - |
Edit
Title | ID | Data type | Description | Examples | Inverse |
---|---|---|---|---|---|
has cause | P828 | Item | cause: underlying cause, thing that ultimately resulted in this effect | mercury poisoning <has cause> mercury | has effect |
has immediate cause | P1478 | Item | cause: 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'. | malaria <has immediate cause> Culicidae | immediate cause of |
has contributing factor | P1479 | Item | contributing 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 Sumner | contributing factor of |
immediate cause of | P1536 | Item | cause: immediate effect of this cause | American Civil War <immediate cause of> assassination of Abraham Lincoln | has immediate cause |
contributing factor of | P1537 | Item | contributing factor: thing 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 disease | has contributing factor |
has effect | P1542 | Item | effect and cause: effect of this item | mercury <has effect> mercury poisoning | has cause |
References Edit
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 administration | P636 | Item | route of administration: path by which a drug, fluid, poison, or other substance is taken into the body | aspirin <route of administration> intramuscular injection | - |
symptoms and signs | P780 | Item | symptom: possible symptoms or signs of a medical condition | meningitis <symptoms and signs> headache | - |
disease transmission process | P1060 | Item | pathogen transmission: process by which a pathogen is transmitted, equivalent to "transmitted by" in the relation ontology http://purl.obolibrary.org/obo/RO_0002451 | influenza <disease transmission process> airborne transmission | - |
population | P1082 | Quantity | number of individuals and human population: number of people inhabiting the place; number of people of subject | San Francisco <population> 892,533 | - |
prevalence | P1193 | Quantity | prevalence: portion in percent of a population with a given disease or disorder | Huntington's disease <prevalence> 0.000123 | - |
manner of death | P1196 | Item | manner of death: general circumstances of a person's death; e.g. natural causes, accident, suicide, homicide, etc. Use 'cause of death' (P509) for the specific physiological mechanism, e.g. heart attack, trauma, pneumonia etc. | Adolf Eichmann <manner of death> capital punishment | - |
number of injured | P1339 | Quantity | injury: number of people with non-fatal injuries in an event | September 11 attacks <number of injured> 6,000 | - |
number of missing | P1446 | Quantity | number of people missing after an event - qualify with "point in time (P585)" | 2013 Lushan earthquake <number of missing> 23 | - |
number of survivors | P1561 | Quantity | number of people surviving an event | Essing bridge accident <number of survivors> 1 | - |
number of casualties | P1590 | Quantity | number 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 cases | P1603 | Quantity | number of infected: cumulative number of confirmed, probable and suspected occurrences | Western African Ebola virus epidemic <number of cases> 13,703 | - |
side effect | P1909 | Item | side effect and adverse drug reaction: effect of a medication or procedure, that occurs next to the desired effect | influenza vaccine <side effect> sore throat | - |
half-life | P2114 | Quantity | half-life: time required for the amount of something to fall to half its initial value | uranium-235 <half-life> 704,000,000 annum | - |
life expectancy | P2250 | Quantity | life expectancy: average life expectancy for this group or species | Pug <life expectancy> 13.5 year | - |
event interval | P2257 | Quantity | recurring entity: standard nominal interval between scheduled or regularly recurring events. Include unit of time, e.g. "year" (Q577). 1/(event frequency). time period of periodically occurring event | Olympic Games <event interval> 4 year | - |
minimal lethal dose | P2300 | Quantity | lowest 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 conditions | acetone <minimal lethal dose> 45.455 parts per million | - |
incidence | P2844 | Quantity | incidence: probability of occurrence of a given condition in a population within a specified period of time | hepatitis C <incidence> 0.5 cases per 100000 person-years | - |
disease burden | P2854 | Quantity | disease 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 constraints Edit
Title | ID | Data type | Description | Examples | Inverse |
---|---|---|---|---|---|
stated in | P248 | Item | reference: to be used in the references field to refer to the information document or database in which a claim is made; for qualifiers use P805; for the type of document in which a claim is made use P3865 | → Property talk:P248 | - |
PubMed ID | P698 | External identifier | PubMed ID and PubMed: identifier for journal articles/abstracts in PubMed | A Study of Variables Affecting the Quality of Platelets Stored at “Room Temperature” <PubMed ID> 823 | - |
DOI | P356 | External identifier | digital object identifier: serial code used to uniquely identify digital objects like academic papers (use upper case letters only) | Ecological guild evolution and the discovery of the world's smallest vertebrate <DOI> 10.1371/JOURNAL.PONE.0029797 | - |
inventory number | P217 | String | accession number: identifier for a physical object or a set of physical objects in a collection | The Night Watch <inventory number> SK-C-5 | - |
reference URL | P854 | URL | URL: should be used for Internet URLs as references. Use "Wikimedia import URL" (P4656) for imports from WMF sites | George Washington <reference URL> http://cths.fr/an/prosopo.php?id=107557 | - |
imported from Wikimedia project | P143 | Item | Wikimedia Foundation project: source of this claim's value; used in references section by bots or humans importing data from Wikimedia projects | → Property talk:P143 | - |
PubMed Health | P653 | External identifier | PubMed: identifier for a physiological condition, in the PubMed Health website | myocardial infarction <PubMed Health> PMH0001246 | - |
related property | P1659 | Property | related property: used to indicate another property that might provide additional information about the subject | website account on <related property> Twitter username and Facebook ID | - |
Other Edit
Title | ID | Data type | Description | Examples | Inverse |
---|---|---|---|---|---|
property constraint | P2302 | Item | property constraint: constraint applicable to a Wikidata property | IMDb ID <property constraint> distinct-values constraint | - |
exception to constraint | P2303 | Item | item that is an exception to the constraint, qualifier to define a property constraint in combination with P2302 | traffic sign <exception to constraint> Shin-Tomei Expressway | - |
group by | P2304 | Property | GROUP BY: qualifier to define a property constraint in combination with P2302 (Wikidata property constraint) that is used to group constraint violations in constraint violation reports | → Property talk:P2304 | - |
item of property constraint | P2305 | Item | allowed-entity-types constraint: qualifier to define a property constraint in combination with "property constraint" (P2302) | mass <item of property constraint> kilogram | - |
property | P2306 | Property | Wikidata 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 | - |
Wikimedia Commons namespace | P2307 | String | qualifier used with the Commons link property constraint (Q21510852) to specify acceptable Wikimedia Commons namespaces that a property value can link to | → Property talk:P2307 | - |
class | P2308 | Item | class: qualifier to define a property constraint in combination with "property constraint" (P2302) | → Property talk:P2308 | - |
relation | P2309 | Item | relation 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) | P2310 | Point in time | qualifier to define a property constraint in combination with "property constraint" (P2302) | → Property talk:P2310 | - |
maximum date (property constraint) | P2311 | Point in time | qualifier to define a property constraint in combination with "property constraint" (P2302). Use "unknown value" for current date. | → Property talk:P2311 | - |
maximum value | P2312 | Quantity | maximum: qualifier to define a property constraint in combination with P2302. "no value" can be used to specify no upper bound | range constraint <maximum value> 1,234 | - |
minimum value | P2313 | Quantity | minimum: qualifier to define a property constraint in combination with P2302 | range constraint <minimum value> 0 | - |
comment (DEPRECATED) | P2315 | Monolingual text | to be deleted: replace with "syntax clarification" (P2916) or add the usage note in the items description. | → Property talk:P2315 | - |
constraint status | P2316 | Item | Wikidata constraint status: qualifier 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 |
---|---|---|---|---|---|
follows | P155 | Item | follows: immediately prior item in a series of which the subject is a part, preferably use as qualifier of P179 [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 Hope | followed by |
followed by | P156 | Item | followed by: immediately following item in a series of which the subject is a part, preferably use as qualifier of P179 [if the subject has been replaced, e.g. political offices, use "replaced by" (P1366)] | March <followed by> April | follows |
applies to part | P518 | Item | part, aspect, or form of the item to which the claim applies | Lady with an Ermine <applies to part> painting support | - |
start time | P580 | Point in time | start time: time an entity begins to exist or a statement starts being valid | Japan <start time> | - |
end time | P582 | Point in time | end time: time an entity ceases to exist or a statement stops being valid | Baroque <end time> 1750s | - |
point in time | P585 | Point in time | point in time: time and date something took place, existed or a statement was true | 2012 United States presidential election <point in time> | - |
of | P642 | Item | (This property is being deprecated, see details at WD:P642) qualifier stating that a statement applies within the scope of a particular item | → Property talk:P642 | has quality |
cause of destruction | P770 | Item | cause of destruction: item which caused the destruction of the subject item | Colossus of Rhodes <cause of destruction> earthquake | destroyed |
separated from | P807 | Item | subject was founded or started by separating from identified object | Presbyterian Church in America <separated from> Presbyterian Church in the United States | merged into |
excluding | P1011 | Item | exception: usually used as a qualifier | British Islands <excluding> Republic of Ireland | - |
including | P1012 | Item | usually used as a qualifier | 2015 San Bernardino shooting <including> suspect | - |
criterion used | P1013 | Item | criterion and declared deserted: property by which a distinction or classification is made | north <criterion used> direction | - |
product or material produced or service provided | P1056 | Item | product: material or product produced by a government agency, business, industry, facility, or process | Jaduguda Uranium Mine <product or material produced or service provided> uranium | - |
proportion | P1107 | Quantity | proportion: to be used as a qualifier, value must be between 0 and 1 | mayonnaise <proportion> 0.7 | - |
quantity | P1114 | Quantity | number of objects: number of instances of this subject in the universe of the subject (the actual number of instances in Wikidata may be lower or higher) | U.S. state <quantity> 50 | - |
valid in period | P1264 | Item | time period when a statement is valid | Tübingen <valid in period> standard time | - |
facet of | P1269 | Item | aspect: topic of which this item is an aspect, item that offers a broader perspective on the same topic | water (data page) <facet of> water | - |
ranking | P1352 | Quantity | ranking: subject's ordinal position as qualitatively evaluated relative to other members of a group | Xu Xin <ranking> 1 | - |
replaces | P1365 | Item | replaced entity: person, state or item replaced. Use "structure replaces" (P1398) for structures. Use "follows" (P155) if the previous item was not replaced or predecessor and successor are identical | Barack Obama <replaces> George W. Bush | replaced by |
replaced by | P1366 | Item | replacing entity: other person or item which continues the item by replacing it in its role. Use P156 ("followed by") if the item is not replaced nor identical, but adds to the series (e.g. books in a series). | Ptolemy XII Auletes <replaced by> Cleopatra | replaces |
definition domain | P1568 | Item | domain of a function: set of "input" or argument values for which a mathematical function is defined | square function <definition domain> set of real numbers | - |
Wikidata property | P1687 | Property | Wikidata property: main Wikidata property for this item | academic discipline <Wikidata property> studied by | Wikidata item of this property |
measurement scale | P1880 | Item | measurement scale: scale by which a phenomenon is measured | earthquake <measurement scale> Richter scale | - |
relative to | P2210 | Item | reference point: qualifier: what a statement value is relative to | Zugspitze <relative to> Normalhöhennull | - |
intended public | P2360 | Item | target audience: this work, product, object or event is intended for, or has been designed to that person or group of people, animals, plants, etc | Naive Set Theory <intended public> teenager | - |
results | P2501 | Item | results of a competition such as sports or elections | 2015 Schaal Sels <results> general classification of the 2015 Coupe Sels | classification of race |