User:ProteinBoxBot/Disease items

Introduction

The ProteinBoxBot maintains information about Genes, Diseases and Drugs in Wikidata. The entities in these three domains are maintained by different corresponding sub-processes of the main bot.

The objective of the Disease sub-process (sub-bot?) is to add and update Wikidata with information about human diseases

Current Scope

The set of entities maintained by this bot are determined based on their presence in the expert-curated Human Disease ontology

Items maintained by this bot

• Human Diseases and classes of human disease. List them all with a query for items with some value for Disease Ontology ID: CLAIM[699]

Properties maintained by this bot for these items

Property	Description	Datatype	Expected value (if not listed, see property definition)
Property:P279	subclass of	Item	Should always include disease (Q12136)
Property:P699	Disease Ontology ID	String	Should exist for EVERY item processed by this bot
Property:P1550	Orphanet	String
Property:P494	ICD-10	String
Property:P493	ICD-9	String
Property:P486	MeSH ID	String
Property:P1395	National Cancer Institute ID	String
Property:P1748	NCI Thesaurus ID	String

Data sources

• Disease ontology

Bot approval

Bot approval August 2015: Wikidata:Requests_for_permissions/Bot/ProteinBoxBot_3

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.

 Approved--Ymblanter (talk) 09:10, 7 August 2015 (UTC)

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ProteinBoxBot 3

ProteinBoxBot (talk • contribs • new items • new lexemes • SUL • Block log • User rights log • User rights • xtools)
Operator: 'Andra Waagmeester (talk)

Task/s: Add disease information from the disease ontology to Wikidata and subsequently enrich these items with relevant additions from authoritative resources.

Code: The ProteinBoxBot contains a core module which takes care of the generic handling of adding and updating of items on wikidata for all current and future tasks. Each task requires a resource specific module. The module for the Disease ontology :code on bitbucket

Function details: The ProteinBoxBot is core in our efforts to enrich wikidata with Genes, Proteins, Diseases, Drugs and the relationships between them. We currently have code in place to enrich wikidata with content from entrez gene and Disease ontology. With the previous bot credentials this code has added human and mouse genes as well as the diseases in the disease ontology. The items have also been updated regularly. We now understand that part of these tasks have been performed out of the scope of the initial bot approval. We would like to request an approval the task to add content from the Disease ontology. The implemented bot takes disease classes related the external from the disease ontology and adds/updates them as Wikidata items. In the near future the bot will also add pubmed references and maintain links to the English wikipedia.

--Andrawaag (talk) 07:27, 26 July 2015 (UTC)

•  Support. Original issues were fixed. Bot is ready to run again. Emitraka (talk) 10:44, 26 July 2015 (UTC)
•  Support. The bot is functional and waiting to add useful content. See test edits. Please approve. I9606 (talk) 16:21, 27 July 2015 (UTC)
•  Support. I fully support adding this information to Wikidata and can easily imagine many projects taking advantage of it. Egon Willighagen (talk) 22:16, 27 July 2015 (UTC)
•  Support. Yes. Multichill (talk) 16:40, 28 July 2015 (UTC)
•  Support Andrew Su (talk) 16:05, 29 July 2015 (UTC)

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The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made in a new section.

Implementation

The bot code is open source and available for inspection.