User talk:Pleiotrope

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Welcome![edit]

Hi. Great to have you aboard the Gene Wiki project! If I can help in any way in getting you started, don't hesitate to ask. Cheers. Boghog (talk) 18:34, 1 April 2011 (UTC)

Thanks for the warm welcome! Looking forward to contributing :) Pleiotrope (talk) 19:56, 1 April 2011 (UTC)

ProteinBoxBot edit summaries[edit]

Could you please take a look at Wikipedia:Bot owners' noticeboard#General notice to bot owners about edit summaries and see if the suggestions might apply to your bot? Feel free to add your own suggestions and comments there too. Headbomb {talk / contribs / physics / books} 21:20, 21 August 2011 (UTC)

Yes, they absolutely do apply- the current bot summaries are somewhat less than helpful. I'll expand it so that the next time the bot updates it'll use more expressive edit summaries. Thanks for giving me the heads up. Pleiotrope (talk) 16:28, 23 August 2011 (UTC)

Creation of new Gene Wiki articles[edit]

Hi. Thanks for your recent bot runs to create new Gene Wiki articles (10,000 down, 10,000 to go! ;-).

Before you make a new run, I do have a couple of requests:

Lead sentence – as discussed here and here, we have tried to make clear that these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human. Since much of the text in these articles focus on the properties of the protein (structure, function, interactions with other proteins), I think it is appropriate that emphasis in the lead is on the protein. Hence I would appreciate if you would reword the lead sentence according to the above suggestion.

Citations – the following should be removed:

  • There are a lot of "'" stray characters imbedded in the citations
  • Empty citations – {{cite journal |author= |title= |journal= |volume= |issue= |pages= |year= |pmid= |doi= }}
  • Large scale sequencing projects that list many genes. These should be "black listed" (e.g., PubMed, PubMed, PubMed, and PubMed).

Stub template – it would be appropriate to add a {{gene}} stub template to the end, for example, if the human gene is located on chromsome 4, please add {{gene-4-stub}} to the end.

See diff for an example.

Talk page – Finally it would be helpful if the following were added to the talk page:

{{WikiProjectBannerShell| {{Wikiproject MCB|class=stub|importance=Low}} {{WikiProject Gene Wiki|class=stub|importance=Low}} }}

Cheers. Boghog (talk) 18:22, 8 September 2011 (UTC)

Thanks for the pointers! I'm in the process of re-writing the stub generator now, so I'll be sure to incorporate these changes before any more stubs are created. Pleiotrope (talk) 18:42, 8 September 2011 (UTC)
I'm setting the filter to omit any projects that reference more than 100 genes. Would you agree with this filter level? Pleiotrope (talk) 00:48, 13 September 2011 (UTC)
This seems like a reasonable number. There may be a few relevant citations that might be filtered out using this cutoff (false positives), but this is likely to be far exceeded by the number of low relevance citations (true negatives). Boghog (talk) 01:24, 13 September 2011 (UTC)

ProteinBoxBot edit request[edit]

Hi,

I've placed a request on the Gene Wiki portal discussion page for ProteinBoxBot to fill in the name parameter of the infoboxes it updates as part of an enhancement of the {{PBB}} template. Any help you can provide would be much appreciated. Thanks! Chris Cunningham (user:thumperward) - talk 09:27, 15 September 2011 (UTC)

Your message[edit]

Thank you for answering my request here. I dropped you a quick answer. Thanks. Anthere (talk) 14:14, 29 September 2011 (UTC)

A barnstar for you![edit]

Vitruvian Barnstar Hires.png The Technical Barnstar
Thanks for improving thousands of pages about human genes with the gene wiki bot updates! Benjamin Good (talk) 15:48, 18 October 2011 (UTC)

IUPHAR parameter[edit]

Hi. The Protein Box Bot has done a great job in maintaining the PBB templates. I do have one additional request. There is a parameter called IUPHAR that if set to yes generates an external link to the IUPHAR database of receptors, ion channels, and nuclear receptors. BogBot had added these parameters to a number of templates, but unfortunately these were overwritten by the Protein Box Bot. I still had a copy of the bot script that added these parameters, so I reran the script to add back the parameter to the appropriate templates (see for example diff).

I would appreciate if Protein Box Bot would check for the presence of this parameter, and if found, preserve it. This parameter that was previously undocumented, but I have just documented it (see Template:GNF_Protein_box#IUPHAR). Cheers. Boghog (talk) 07:37, 17 November 2011 (UTC)

Hi Boghog, I'll add that behavior into ProteinBoxBot today. Thanks for pointing that out and documenting it. Pleiotrope (talk) 16:14, 17 November 2011 (UTC)

Ping[edit]

Nuvola apps edu languages.svg
Hello, Pleiotrope. You have new messages at Template_talk:GNF_Protein_box.
Message added Boghog (talk) 22:02, 28 January 2012 (UTC). You can remove this notice at any time by removing the {{Talkback}} or {{Tb}} template.
Nuvola apps edu languages.svg
Hello, Pleiotrope. You have new messages at Template_talk:GNF_Protein_box.
Message added Boghog (talk) 22:02, 28 January 2012 (UTC). You can remove this notice at any time by removing the {{Talkback}} or {{Tb}} template.

Invitation to events: bot, template, and Gadget makers wanted[edit]

I thought you might want to know about some upcoming events where you can learn more about MediaWiki customization and development, extending functionality with JavaScript, the future of ResourceLoader and Gadgets, the new Lua templating system, how to best use the web API for bots, and various upcoming features and changes. We'd love to have power users, bot maintainers and writers, and template makers at these events so we can all learn from each other and chat about what needs doing.

Check out the Chennai event in March, the Berlin hackathon in June, the developers' days preceding Wikimania in July in Washington, DC, or any other of our events.

Best wishes! - Sumana Harihareswara, Wikimedia Foundation's Volunteer Development Coordinator. Please reply on my talk page, here or at mediawiki.org. Sumanah (talk) 15:25, 16 February 2012 (UTC)

You might especially be interested in coming to the Berlin event, as it will have a strong emphasis on structured/semantic data. Hope to see you there! Sumanah (talk) 15:26, 16 February 2012 (UTC)

PBB/28[edit]

Hi Pleiotrope, The ProteinBoxBot is replacing Uniprot P16442 with C3VA45 (an unreviewed fragment) for the human protein in PBB/28. As a result the PDBs are stripped out as the structures are mapped to P16422 not C3VA45. Can anything be done about this? Thanks A2-33 (talk) 19:31, 3 April 2012 (UTC)

Hi A2-33, thanks for bringing this to my attention. PBB should check for reviewed entries before updating, so I'll fix this bug before the bot updates again. Please let me know if there are any other issues you notice. Cheers, Pleiotrope (talk) 19:40, 3 April 2012 (UTC)
Following up: I've fixed the issue you've referred to. The bot now checks with Uniprot directly if it can't find a reviewed accn number from its primary source. In the future, if you notice an edit you make getting overwritten, you can add the {{nobots}} template until the bug gets fixed. Cheers, Pleiotrope (talk) 04:40, 4 April 2012 (UTC)

GeneWikiGenerator not creating pages[edit]

Hi. For quite some time, the GeneWikiGenerator no longer is able to create new Gene Wiki articles and templates. The Generator still creates the template and article code, but when one clicks the "create page" button, nothing happens. Is the Wikipedia bot that creates these pages still logged on? I would appreciate if you would check this when you get a chance. There is a growing list of requests. Thanks. Boghog (talk) 04:26, 11 April 2012 (UTC)

Hi Boghog, I've fixed the bug. Thank you for letting me know, and don't hesitate to ping me asap if you notice it not working in the future. Note: it's currently working but will not display a confirmation message when the article is created. Refreshing the page should show the updated results. I'll have a fix for that soon, but feel free to use it in the meantime. Pleiotrope (talk) 04:57, 11 April 2012 (UTC)

ChEMBL links[edit]

Per this discussion, I have started adding ChEMBL links to GNF_Protein_box templates. I would appreciate if you would modify the Protein box bot so this parameter is not over written. Thanks. Boghog (talk) 04:47, 4 May 2012 (UTC)

Fixed, thanks for letting me know. Pleiotrope (talk) 21:51, 7 May 2012 (UTC)

Collaboration with NCBI?[edit]

Hi, I would appreciate your opinion on opportunities to collaborate with NCBI. Thanks, -- Daniel Mietchen - WiR/OS (talk) 02:20, 19 July 2012 (UTC)

ProteinBoxBot[edit]

Your bot, ProteinBoxBot, uploaded a bundle of images a few years ago (eg. File:PBB Protein INDO image.jpg) with no description. There looks to be about 50 or so that are populating in Category:Wikipedia files lacking a description. I was wondering if there would be a way for you or your fellow bot owner to get the bot to go and add a description to the files. (I will also be posting on your bot co-owner's talk page) Thanks in advance. -- ТимофейЛееСуда. 21:57, 4 September 2012 (UTC)

Template:PBB[edit]

I've asked a question at Template talk:PBB#Just a hardcoding? but not received a response. As one of ProteinBoxBot's operators, I'm wondering if you can shed a light on it for me. VanIsaacWS Vexcontribs 07:59, 30 July 2013 (UTC)

Please see my comment at User talk:Andrew Su#PBB templates.—Anomalocaris (talk) 19:00, 26 September 2013 (UTC)

ProteinBoxBot updates to UniProt links[edit]

Hi. ProteinBoxBot is making a large number updates that seem to be in error. See for example diff. Regards Boghog (talk) 10:41, 15 November 2013 (UTC)

In the meantime, I have requested a temporary emergency shutdown of the bot. Boghog (talk) 11:04, 15 November 2013 (UTC)