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Drug and chemical compound items in Wikidata as a data source for Wikipedia infoboxes
https://commons.wikimedia.org/wiki/File:Wikidata-logo-en.svg
Sebastian Burgstaller-Muehlbacher, PhDUser:SeboticTwitter: @sebotic
Contents
The Problem
Introduction to WikidataData model
References
Values/data types
Gene Wiki Info Boxes - An Example solution
Chemistry Data in WikidataIssues with the data
Community cleanup
Migration of Info Boxes to Wikidata
The Problem (with chemistry data)
Wikipedia has ~300 different languages projects
Currently, chemistry data resides as info box parameterData are not reusable between language projects
Data are not machine readable
Data are hard to update automatically
Data cannot be reused for other purposes, e.g. science.
The solution
-Labels, descriptions, aliases in different languages
-Diverse Properties
-Sitelinks
Wikidata items
Two types of entitiesProperties (Pxxxx): Describe the nature of a data value
Different data types
2,900 different properties in Wikidata
Data items (Qxxxx): A set of claims or statements
Consist of property value pairs
20 million items in Wikidata
-Properties must be proposed and approved by the community
-Data items can be edited by any Wikidata user and are the true data stores.
A Wikidata Statement
https://commons.wikimedia.org/wiki/File:Wikidata_statement.svg
Claim: Property with value + optional qualifiers
Statement: A claim with its references
Wikidata Data types
The current Wikidata data types: String
WDItemID
External ID
MonolingualText
Property
Quantity
Time
Url
GlobeCoordinate
CommonsMedia
Mathematical formula
-Many querys to the Wikidata API make the bot slow and might make Wikimedia people/adminstrators unhappy.
-Calling wbeditentity ensures that all data is either written or not, so if the connection or bot breaks, no harm is done. -No new items will be created and then left unpopulated.
Unique Features of Wikidata
Completely free, even for commercial usage (CC0).
Granular: Single values with references.
Anybody can contribute.
Extensive item history.
A repository for data on all domains of knowledge.
Full integration with the semantic web.
Essentially: A giant graph of knowledge.
Single value refs/nano publications
Revisions/data releases
Burgstaller-Muehlbacher, et al, Database, 2016
Data use case: Gene Wiki infoboxes
Issues with chemical data in the Wiki space
Incorrect identifiers in info boxes or on Wikidata items
Incorrect chemical properties
Incorrect labels, aliases
Incorrect isomeric forms of the compound
Mixture of different isomeric forms
https://commons.wikimedia.org/wiki/File:Isomerism.svg
How to solve Isomerism issues?
Make sure that the structure in Wikidata and Wikipedia are correct and consistent:Use the InChI (International Chemical Identifier) or InChI key to determine what isomer a certain article or WD item is actually talking about.
What are InChIs
IUPAC InChI (International Chemical Identifier).
Describes the structure of a chemical compound or substance.
Freely usable.
Can be computed from e.g SMILES, or MOL format.
Do not need to be assigned by an organization.
What are InChI keys
The SHA-256 hashed version of an InChI
Makes chemicals searchable on the Web
Makes chemicals easily comparable
Short, unique
UEJJHQNACJXSKW-UHFFFAOYSA-N
First block (14 letter) encodes skeleton (connectivtiy)
Second block (8 letter) encodes stereochemistry and radioisotopes
Last letter, number of protons (charge)
How to solve Isomerism issues?
Make sure that the structure in Wikidata and Wikipedia are correct and consistent:Use the InChI (International Chemical Identifier) or InChI key to determine what isomer a certain article or WD item is actually talking about.
Minimum requirement: Correct, unique InChI key on item.
Best case: Make sure all structural identifiers are correct (isomeric SMILES, canonical SMILES, InChI or InCh key).
A minimum of a correct InChI key allows for the rest of the chemical compound item to be populated by (our) bots.
What has been accomplished so far?
Discussion on Wikiproject chemistry: https://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry#Wikidata_as_source_for_infobox_dataGeneral consensus that info boxes should use Wikidata
Wikidata needs to improve on data quality
Of the 17,000 original chemical compound Wikidata items, 16,000 have been validated around an InChI key.
More chemical data has been imported, so they are readily available for new Wikipedia articles or correction of existing ones.
Things that need your attention
I generated a list of items at Wikidata project chemistry which need human intervention.
https://www.wikidata.org/wiki/Wikidata_talk:WikiProject_Chemistry#Annotation_in_which_species_chemical_compounds_are_found
Please have a look at those and unify the sterechemistry and identifiers around one unique InChI key!
Data maintenance in Wikidata
Our bots are written in Python (2.7 and 3.x compatible).
Python bots keep Wikidata in sync with authoritative data source. (PubChem, ChemSpider, ChEBI, ChEMBL)
Bots are run according to data release cycles of authoritative data sources.
Mechanisms in place for detection of inconsistencies.
Contributions of other Wikidata users are being accounted for, based on references.
Wikidata API and query endpoints
Three ways to access data:Wikidata API allows read, write and full text search. (www.wikidata.org/w/api.php)
REST endpoint for fast, direct data access.
(queryr.wmflabs.org/)
Wikidata query service (WDQS) as a SPARQL endpoint for complex
queries.
(query.wikidata.org/)
The Sparql endpoint allows complex and also federated queries on the full WD content.
REST and SPARQL are still in beta mode.
Acknowledgments
Andrew SuBenjamin GoodTim PutmanJulia TurnerGregg
Stupp(TSRI)
Gang Fu Evan Bolton(NIH, PubChem)
Andra Waagmeester
(Micelio.be)
Elvira Mitraka Lynn Schriml(Disease Ontology, U Baltimore)