Pathwaybot

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Welcome to WikiProject Gene Wiki This page documents the Pathway bot, that it is maintained within the Wikiproject Gene Wiki. It is a WikiProject dedicated to make and maintiain Wikidata as a central hub of linked knowledge on Genes, Proteins, Diseases, Drugs, and related concepts.

This user account is a bot with a bot flag. The bot is operated by mkutmon  and Andrawaag. Block this bot if it is malfunctioning. Check its work. Contact the operator about mistakes. See all Requests for Permissions related to this bot: 1 License:

Purpose

The objective of this bot is to provide Wikidata with up-to-date high quality information about Pathways and the interactions between the pathway entities they contain. This bot is under development and is being based on the code base of the User:ProteinBoxBot.

The team

• Alexander Pico (WikiPathways)
• Andra Waagmeester (Genewiki, Scholia profile)
• Sarah Keating (Reactome)
• Egon Willighagen (WikiPathways, Scholia profile)
• Denise Slenter (WikiPathways)
• Benjamin Good (Genewiki)
• Chris Evelo (WikiPathways, Scholia profile)
• Martina Summer-Kutmon (WikiPathways)

Discussion documents

• Discussing WikiPathways in Wikidata

Sources

• WikiPathways
• Reactome

Legalities

WikiPathways will be the first pathway repository sourced by this bot. Currently WikiPathways is available as CC-BY, but to be able to include pathways from WikiPathways into Wikidata, the decision has been made to transition towards a CC0 license. While in transition towards CC0, we have selected the following Pathways to develop and fine tune the pathway bot.

Gameplan

1. agree on the data model <- Done (May 6th, 2017)
2. receive bot permission
3. Add the remaining pathways which are included in Wikipedia articles <- Done (May 11th, 2017)
4. wait a week for community input
5. Run the bot on all human pathways
6. wait a week
7. Request addition of remaining species for those that are not yet covered on Wikidata by ProteinBoxBot
8. Run the bot on the remaining species.
9. Model “part of” manually into data model 2.0
10. Revisit update cycle
11. Model interactions

Bot code

• The bot is based on the Wikidata Integrator platform developed in the Genewiki project.
• The bot code lives on GitHub

Data model

Wikipedia -> Wikidata

Property	Reference properties	Qualifier properties
instance of (P31)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
described by source (P1343)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
+ = required * = optional

WikiPathways

Property	Reference properties	Qualifier properties
instance of (P31)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
WikiPathways ID (P2410)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
found in taxon (P703)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
cites work (P2860)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
has part(s) (P527)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
connects with (P2789)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
+ = required * = optional

Shape expression

PREFIX wp: <https://en.wikipedia.org/wiki/>
PREFIX wd: <https://www.wikidata.org/wiki/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX schema: <http://schema.org/>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX pr: <http://www.wikidata.org/prop/reference/>

start = <wikipathways-pathway_type>
<wikidata-wikipathways-pathway> {
	p:P31	@<P31_instance_of_metabolic-pathway>+ ;
	p:P2410	@<P2410_WikiPathways_ID>{1} ; 
	p:P703	@<P703_found_in_taxon>{1} ;
	p:P2860	@<P2860_cites>* ;
	p:P527	@<P527_has_part>+ ;
}
<P31_instance_of_pathway-type> {
	ps:P31	@<pathway_types>
}
<P527_has_part> {
   ps:P527	@<geneproduct> OR @<metabolite> OR @<protein> ;
   prov:wasDerivedFrom	@<wikipathway_reference> ;
}
<P703_found_in_taxon> {
	ps:P703	@<wikipathway_species> ;
	prov:wasDerivedFrom	@<wikipathway_reference> ;
}
<P2410_WikiPathways_ID> {
	ps:P2410	LITERAL ;
	prov:wasDerivedFrom	@<wikipathway_reference> ;
}
<P2860_cites> {
	ps:P2860	@<pubmed_citation> ;
	prov:wasDerivedFrom	@<wikipathway_reference> ;
}
<wikipathway_reference> {
	pr:P248		[wd:Q7999828] ; # P248 stated in, wd:Q7999828 = WikiPathways
	pr:P813		xsd:dateTime ;
	pr:P854		IRI ; # TODO make explicit to recognize only the variant URL e.g. http://www.wikipathways.org/instance/WP179
}
<wikipathways_species> [
	wd:Q15978631 # Homo sapiens
	wd:Q83310	# Mus musculus
	wd:Q184224. # Rattus norvegicus
	# TODO get all species covered in WikiPathways
]
<pubmed_citation> {
	wdt:P31	[wd:Q13442814] # P31 = instance of, Q13442814 = scientific article
	wdt:P698 LITERAL	# P698 = Pubmed ID
}
<pathway_types> [
	wd:Q28864279 # pathway
	wd:Q28864276 # classical metabolic pathway
	wd:Q28864297 # disease pathway
	wd:Q28864298 # drug pathway
	wd:Q28864299 # regulatory pathway
	wd:Q28864300 # signaling pathway
]
<geneproduct> {
# TODO specify
}
<metabolite> {
# TODO specify
}
<protein> {
# TODO specify
}

Source (github)