Wikidata:Requests for permissions/Bot/MicrobeBot
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) 19:41, 30 November 2015 (UTC)[reply]
MicrobeBot edit
MicrobeBot (talk • contribs • new items • new lexemes • SUL • Block log • User rights log • User rights • xtools)
Operator: Putmantime (talk • contribs • logs)
Task/s:
This bot will be an extension of the ProteinBoxBot project, shifting focus to taxa, gene, and protein items for microbial species. We plan to load data for the 120 Bacterial Reference Sequences designated by NCBI as the highest quality and most relevant bacterial genome sequences available.
Code: https://bitbucket.org/sulab/wikidatabots/src
Function details:
Using the same core infrastructure as the ProteinBoxBot, MicrobeBot will import microbial genetic data to Wikidata from NCBI and UniProt using MyGene.info. The data model is illustrated in Figure 1. We have developed the bot in Python and, using this structured model, we have imported the genetic data for 2 strains of Chlamydia trachomatis, totaling 1738 genes and 1741 proteins. The goal is to load, pending community support and approval, the gene and protein items for all of the 120 Bacterial Reference Sequences. This would aggregate the genetic data for the most studied and relevant microbial genomes into integrated and structured Wikidata framework, providing microbial and human researchers a novel tool for making meaningful connections between all genetic and health related entities in Wikidata (i.e. hosts, pathogens, drugs, diseases, etc...).Putmantime (talk) 19:57, 12 November 2015 (UTC)[reply]
- Since the bot was blocked as a spambot I think we need to go for a wider community consensus, for example, by starting a topic at Wikidata:Project chat--Ymblanter (talk) 20:18, 16 November 2015 (UTC)[reply]
- Just to clarify, there was no attempt to create or edit Wikidata items with this bot. The block occurred as I was attempting to populate the user page with information on the bot tasks, while logged into the newly created Microbebot account. I realize now I should have been editing that page from my own user account. Putmantime (talk) 17:01, 17 November 2015 (UTC)[reply]
- This bot is certainly not a spam bot. It would be helpful to know why the AbuseFilter flagged it, though. The work of User:ProteinBoxBot here has been immensely useful, and extending it to microbial genetics makes a lot of sense, so I am all in favour of some test runs. --Daniel Mietchen (talk) 23:47, 17 November 2015 (UTC)[reply]
- Now I unblocked the bot, pls make some test edits.--Ymblanter (talk) 12:51, 18 November 2015 (UTC)[reply]
- I have generated these 20 (10 protein and 10 gene) example items with the MicrobeBot. These edits were made with the ProteinBoxBot account (using MicrobeBot code) . As outlined in Figure 1 the genes and protein items are linked via the encodes (P688) and encoded by (P702) properties, and all are linked to the strain they were sequenced from via the found in taxon (P703) property.
- Strain: Helicobacter pylori 26695 (Q21065231)
- Gene:
- flagellar biosynthesis protein FlhA HP1041 (Q21541794)
- methionine adenosyltransferase HP0197 (Q21541795)
- NADH-quinone oxidoreductase subunit M HP1272 (Q21541796)
- biotin--protein ligase HP1140 (Q21541797)
- alkylphosphonate uptake protein PhnA HP0872 (Q21541798)
- chemotaxis protein CheY HP1067 (Q21541799)
- hemolysin HP1086 (Q21541800)
- flagellar basal body protein FliL HP0809 (Q21541801)
- hypothetical protein HP1328 (Q21541802)
- cbb3-type cytochrome c oxidase subunit III HP0147 (Q21541803)
- Protein:
- Flagellar biosynthesis protein FlhA HP1041 (Q21542453)
- Methionine adenosyltransferase HP0197 (Q21542459)
- NADH-quinone oxidoreductase subunit M HP1272 (Q21542462)
- Biotin--protein ligase HP1140 (Q21542466)
- Alkylphosphonate uptake protein PhnA HP0872 (Q21542467)
- Chemotaxis protein CheY HP1067 (Q21542471)
- Hemolysin HP1086 (Q21542477)
- Flagellar basal body protein FliL HP0809 (Q21542480)
- Hypothetical protein HP1328 (Q21542482)
- Cbb3-type cytochrome c oxidase subunit III HP0147 (Q21542489)
- Putmantime (talk) 22:47, 24 November 2015 (UTC)[reply]
- I have generated these 20 (10 protein and 10 gene) example items with the MicrobeBot. These edits were made with the ProteinBoxBot account (using MicrobeBot code) . As outlined in Figure 1 the genes and protein items are linked via the encodes (P688) and encoded by (P702) properties, and all are linked to the strain they were sequenced from via the found in taxon (P703) property.
- I am going to approve the bot in a couple of days provided there have been no objections raised.--Ymblanter (talk) 22:13, 25 November 2015 (UTC)[reply]