Wikia

Proposal overview (brief version)Edit

This bot will create or amend up to ~10,000 pages corresponding to mammalian genes. Pages will be created in groups of ~100 to ensure page quality. Each new page will be seeded with content from databases in the public domain. This content will include information about the gene's symbol, description, function, genomic location, structure and identifiers. Genes which do not have any existing WP pages for its symbol, aliases, or title will be created (e.g., MMP9). Genes which do have these conflicts in the WP namespace will be flagged for manual integration (e.g., Apolipoprotein_E). More details are presented in User:ProteinBoxBot/Ideas. This bot is currently being designed and developed by AndrewGNF and JonSDSUGrad. The list of all pages which were created or edited with ProteinBoxBot content is shown here.

RequestsEdit

Want an enhanced Protein box for your favorite gene? Feel free to add your request below and we'll bump it to the top of the list. If the target gene page already exists, please wikilink it!

ProteinBoxBot requests
Gene Symbol	Entrez Gene ID	Requestor	PBB completion date
SCXB	642658	163.1.64.145 (talk) 11:24, 23 January 2008 (UTC)
RELN	5649	CopperKettle	30 October 2007
SERPINC1	462	K.murphy	17 November 2007
F10	2159	K.murphy	17 November 2007
TYR	7299	K.murphy	17 November 2007
FGF2	2247	K.murphy	2 November 2007
EPAS1	2034	Clockguy	17 November 2007
HIF3A	64344	Clockguy	17 November 2007
OPN4	94233	Clockguy	17 November 2007
USH1C	10083	Willow	17 November 2007
USH1G	124590	Willow	17 November 2007
USH2A	7399	Willow	17 November 2007
CLRN1	7401	Willow	17 November 2007
MYO7A	4647	Willow	17 November 2007
SLC4A7	9497	Willow	17 November 2007
CDH23	64072	Willow	17 November 2007
PCDH15	65217	Willow	17 November 2007
VLGR1	84059	Willow	17 November 2007
RXRB	6257	Boghog2	17 November 2007
RXRG	6258	Boghog2	17 November 2007
PPARD	9235	Boghog2	17 November 2007
ADRA1A	148	AndrewGNF	17 November 2007
ADRA1B	147	AndrewGNF	17 November 2007
ADRA1D	146	AndrewGNF	17 November 2007
ADRA2A	150	AndrewGNF	17 November 2007
ADRA2B	151	AndrewGNF	17 November 2007
ADRA2C	152	AndrewGNF	17 November 2007
ADRB1	153	AndrewGNF	17 November 2007
ADRB2	154	AndrewGNF	17 November 2007
ADRB3	155	AndrewGNF	17 November 2007
ADRBK1	156	AndrewGNF	17 November 2007
ADRBK2	157	AndrewGNF	17 November 2007
MAP2K7	5609	Lihmwiki	done
MAP3K1	4214	Lihmwiki	done
MAP2K5	5607	Lihmwiki	done
Parkin (ligase)	5071	cmcnicoll
Ubiquitin carboxy-terminal hydrolase L1	7345	cmcnicoll	done
ATP13A2	23400	cmcnicoll	done
HtrA serine peptidase 2	27429	cmcnicoll	done
DFNB31	25861	Willow	done

Trial RunEdit

A trial run for this bot was approved. The trial was completed and the log is here: User:ProteinBoxBot/PBB_Log_Wiki_Live_Run.

After making quite a few adjustments, a second trial run was completed and the log file is here: User:ProteinBoxBot/PBB_Log_Wiki_Live_Run3_Char_Fix

The bot was subsequently approved and granted bot status.

The eight pages created by the ProteinBoxBot in the trial are:

AKT1	HIF1A	MAPK1	MMP9
NFKB1	PPARG	PTGS2	TGFB1

In addition, these pre-existing pages were supplemented with ProteinBoxBot content in a semi-automated edit:

APP	APOE	Androgen receptor	BRCA1
Bcl-2	P21	P16	Beta-catenin
Epidermal growth factor receptor	HER2/neu	Estrogen receptor	HLA-B
Insulin-like growth factor 1	Interleukin 10	IL1B	Interleukin 6
Interleukin 8	CD29	PKC alpha	Retinoblastoma protein
Src (gene)	Tumor necrosis factor-alpha	P53 (protein)	Vascular endothelial growth factor
Caspase 3

The discussion of the ProteinBoxBot's trial run is archived at Wikipedia:Bots/Requests_for_approval/ProteinBoxBot.

Logic Flow Edit

The following Flow charts describe the logic of Protein Box Bot:
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LinksEdit

Protein Box bot does extensive logging of its activities.

Bot Log File: User:ProteinBoxBot/PBB_Log_Index

Protein Box Bot does not always know the exact name of a protein page. This page has been created to help with that.

Bot Page Directory: User:ProteinBoxBot/Protein_Directory

Protein Box Bot Quick ManualEdit

When dealing with wikipages it is often difficult to automatically determine how and what to update - especially for a bot. Therefore a group of templates were created to ensure that Protein Box Bot behaves appropriately and will not overwrite any information without permission. The templates provide update options and editing boundaries. The Templates are described below:

Template: PBB_Controls (Required)Edit

PBB_Controls does not display any information on the gene page, instead its sole purpose is to allow update options for PBB. PBB cannot update a gene page that is missing this template. (See the template page for further details)

Template: PBB_Summary Edit

This template contains the entrez summary for the gene. If no summary is available, then this template is left blank. It is suggested that a blank template be left on the gene page to provide a location for possible future summary updates. During an update, all information in this template is overwritten. See Template:PBB_Summary for more information.

Template: GNF_Protein_boxEdit

The GNF_Protein_Box is the core template updated by PBB. The majority of the information provided by PBB is places in this protein. While it is possible to exclude this template from a gene page, it is not recommended.
During an update, all information in the protein box is overwritten (even with blank values) with the exception of 'image' and 'image_source', which are carried over into the new box. Only if those fields are blank will the Bot try and locate an image. Default image file names follow this format: </p>

PBB_Protein_<protein symbol>_image.jpg

Where <protein symbol> is the actual symbol for the protein (such as PBB_Protein_AKT1_image.jpg).

Template: PBB_Further_readingEdit

PBB_Further_reading is the template that PBB uses to store citation information. All entries within this template are overwritten when PBB does an update.

TAG: No Bots (Optional)Edit

<!-- NO BOT EDITS -->

OR

{{nobots}}

This tag will cause the bot to skip updating this page. As the presence of this tag will abort the operation of the bot, its use is optional and not required for bot operation.