Wikidata:Requests for permissions/Bot/UreomiczBot

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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) 20:22, 30 August 2016 (UTC)[reply]

UreomiczBot 1[edit]

UreomiczBot (talk • contribs • new items • new lexemes • SUL • Block log • User rights log • User rights • xtools)
Operator: Egon Willighagen (talk • contribs • logs)

Task/s: The task is to annotate chemical compounds in human metabolic pathways found on WikiPathways as such and to add chemical compounds in those pathways that are not yet in Wikidata. The latter is determined based on the PubChem CIDs given in WikiPathways and the matching InChIKey as provided by PubChem.

Code: The code is available from the feature/metabolites branch on BitBucket.

Function details: The code makes use of the User:ProteinBoxBot code base as found in the wikidatabots project of the Su lab also on BitBucket.

The code first aggregates information:

  1. it retrieves PubChem CIDs for chemical compounds marked "Metabolite" in human pathways in the WikiPathways database
  2. it looks up the SMILES, InChI, and InChIKey using the PubChem PUG REST API
  3. it checks Wikidata for an existing entry with either the PubChem CID or the InChIKey (in that order, consistency is not checked!)
  4. if not existing, it will create (current blocked by an API error) a new item, with label and PubChem CID (with source reference pointing to WikiPathways), and SMILES, InChI, and InChIKey (with source reference pointing to PubChem) and instance of (P31)-ing the entry as a 'chemical compound' 'found in taxon' 'Homo sapiens'
  5. if it does exist, it will only instance of (P31) the entry as a 'chemical compound' 'found in taxon' 'Homo sapiens'

The User:Ureomics/Human_metabolites task page has further information, including on the current test runs. Questions, suggestions, and other forms of feedback are most welcome.

--Egon Willighagen (talk) 13:30, 27 August 2016 (UTC)[reply]

Normally a bot must have the word "bot" in the username: «Bot accounts are generally named after either their operator or their function, combined with the word "bot"» Can you change the name? --ValterVB (talk) 13:54, 27 August 2016 (UTC)[reply]
@ValterVB: Yes, I know. I actually did that, but apparently forgot to write down the password and did not give it an email address (or so it seems). I asked support on #wikidata, but they could not help. So, in fact, User:UreomicsBot exists, but I currently don't have access to it. Once some admin restored my access, I can indeed rename the account. --Egon Willighagen (talk) 14:16, 27 August 2016 (UTC)[reply]
If you have forgot the password none can help you, but you can create a new user (ex. UreomicsBot2 or Ureomics2Bot) --ValterVB (talk) 16:18, 27 August 2016 (UTC)[reply]
OK, done: User:UreomiczBot. I will make a few test edits with that one too. --Egon Willighagen (talk) 18:01, 27 August 2016 (UTC)[reply]
@ValterVB: What is the expected protocol now? Leave this bot (task) request with the original name, open a new request, or rename the bot name mentioned in this request? --Egon Willighagen (talk) 18:38, 28 August 2016 (UTC)[reply]
@Egon Willighagen: You can move this page the to the new name. If you have problem ping me. --ValterVB (talk) 19:00, 28 August 2016 (UTC)[reply]
Done! --Egon Willighagen (talk) 19:09, 28 August 2016 (UTC)[reply]

 Support I really welcome this bot. It is using the same codebase as the ProteinBoxBot. --Andrawaag (talk) 18:09, 27 August 2016 (UTC)[reply]

 Comment User:Wostr pointed out on my Discussion page that found in taxon (P703) can be used directly on the Wikidata entry being added/edited, so, instead of instance of (P31). The provenance model can remain the same then. If there are no objections, I will update the proposal accordingly tomorrow. --Egon Willighagen (talk) 18:49, 27 August 2016 (UTC)  Support I just went through today's test edits, which look good and useful to me. Agree that it's better to use found in taxon (P703) as a property rather than qualifier. --Daniel Mietchen (talk) 13:01, 29 August 2016 (UTC)[reply]

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