User:MicrobeBot

This user account is a bot with a bot flag. The bot is operated by Putmantime, Andrew Su  and Djow2019. 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:

Introduction

The objective of the MicrobeBot is to add and update Wikidata with information about genes and proteins of microbial origin. A discussion has been initiated on the Project Molecular Biology Talk Page

Figure 1. A microbial gene item in Wikidata (blue) and the structure of its linkage (through QIDs and properties) to the organism item of origin (green) and the protein item it encodes (orange). Solid black lines indicate WD Properties.

Sister Bots

ProteinBoxBot

Bot tasks and state

MicrobeBot will provide WikiData with up-to-date high quality information about microbial taxa, genes, gene-products and other annotations from authoritative sources. These concepts will form the backbone upon which many biomedical applications of WikiData will be based. The open source bot code is divided into a collection of tasks. These tasks consist of establishing taxonomic links between species and strains of bacteria, or creating those entities if they do not yet exist. The next level of tasks focuses on creating items for genes and gene-products and linking them to the strain they were sequenced from. Finally, the gene and gene-products are linked together. All bot edits are based on content from trusted, manually curated scientific resources. For additional information about each bot task, follow the links in the status table below.

Bot task	Discussion started	Coding and testing	Production ready	Is approved	Is running	update frequency	last full cycle
Microbial gene and protein items	x	x	x	x	x
...

Current Scope

The set of entities maintained by this bot are determined based on their presence in the expert-curated NCBI Entrez Gene database.

At present, the bot is limited to genes and proteins from bacteria and will be expanded to include microbial genes of non-bacterial origin.

Items maintained by this bot

• Bacterial Strains, Genes, and Gene-Products. Lists them all with a query for items with taxon bacteria and some value for Entrez Gene ID:

Gene properties planned for this bot

Property	Description	Datatype	Expected value (if not listed, see property definition)
P279	subclass of	Item	Should always include gene (Q7187)
P351	Entrez Gene ID	String	Should exist for EVERY item processed by this bot. Property will include concurrent Entrez IDs for each strain of bacterial species
P644	Genomic start	String	Should exist for EVERY item processed by this bot. Property will include concurrent Genomic starts for each strain of bacterial species
P645	Genomic end	String	Should exist for EVERY item processed by this bot. Property will include concurrent Genomic ends for each strain of bacterial species
P703	found in taxon	Item	Will include the bacterial strain item that the gene was sequenced from
P688	encodes	Item

The 'encodes' property links gene items to items specifically about the protein, RNA, or other 'product' of the gene. A single gene corresponds to a particular region of a genome that is related to some set of functions. These functions are carried about by the gene's products. Different products may perform vastly different functions. Hence we separate functional information from the gene item itself, and attach this information to the product items wherever possible. (See Proposal for bringing microbial genome, gene, and protein items to Wikidata)

Protein properties Planned for this bot

Property	Description	Datatype	Expected value (if not listed, see property definition)
P279	subclass of	Item	One of: Protein (Q8054), RNA (Q11053), non-coding RNA (Q427087), ..
P702	encoded by	Item	Should exist for EVERY item processed by this bot
P352	UniProt ID	String	Should exist for EVERY item processed by this bot
P638	PDB ID	String
P637	RefSeq Protein ID	String
P705	Ensembl Protein ID	String
P681	Cell Component	Item
P682	Biological Process	Item
P680	Molecular Function	Item

Data sources

The bot will retrieve its content from the following trusted sources:

• mygene.info - is a Web service that integrates and provides a convenient API for information about all genes . It provides data from Entrez Gene and other authoritative sources
  • Data will also be loaded from
    1. NCBI Bacterial Annotation Release 70 (Q20819119)