User:ProteinBoxBot/Ideas

NOTE: This page is effectively read-only, except by the bot organizers. Please post any ideas and suggestions on the discussion page.

Development plan and future ideas

NOTE: The items below are thoughts for the future and are not included in the initial proposed specs.

See also: User:ProteinBoxBot/Project_proposals

Next up for implementation

• per discussion on Commons, add PDB infobox to all PDB images (Example [1])
• Run bot update
  • needs to work with new data Web services
  • remove {{PBB_Summary}} and {{PBB_Controls}} from main namespace
    • blocking edits to {{PBB}} templates can use the generic {{nobots}}
• pilot project for {{SWL}}
  • find some well-known facts
  • encode them in Gene Wiki article using {{SWL}}
  • figure out synchronization with wikidraft.org/SMW, converting SWLs to real semantic links
  • OUTPUT: demonstrate real inline queries on wikidraft.org
  • OUTPUT: export from SMW to RDF
• pilot collaboration with MODs (specifically ZFIN)
  • scan through all Gene Wiki pages for inline citations
  • retrieve MeSH terms identify matching species (human, mouse, zebrafish, fly, rat, yeast)
  • generate four-column output file:

1. WP article name
2. cited pubmed ID
3. matching organisms by MeSH
4. sentence(s) referencing the publication

• Notes

• is there a MeSH-to-taxonomy mapping? or do free-text matching?
• for pubs that reference multiple species, one line per species
• for articles that reference a pub multiple times, concatenate sentences

• redesign infobox to better handle linking to MODs (MGD, RGD, ZFIN, FlyBase, WormBase, etc.)

Add additional links

• GeneCards
• nextbio.com?
• wikiprofessional
• wikigenes
• WikiPathways.org
• KEGG (also add wikilinks to other gene pages in the same KEGG pathways)
• HPRD
• link to Bioinformatic Harvester? -- would need community consensus...

Add/improve stub data (gene-specific)

• change format of the references section to make it small-screen friendly ([2])
• Add GeneRIFs and references from Uniprot
• import and display EC number
• import and display protein domain information (through Uniprot/PFAM/COGs) See previous discussion.
• UniProt fields: PFAM, "Protein name", "Synonyms", FUNCTION, DOMAIN, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, and WEB RESOURCE
• Need to fix the db links for genome locations: default for mouse has gone to mm9 User_talk:ProteinBoxBot#Mouse_location_links_lack_db_name_parameter (need to either change default in template, or need to do a second pass run on all infoboxes to add parameter)
• Load PPI from Entrez Gene User_talk:ProteinBoxBot/Archives/Archive1#Interaction_partners
• Add a note in infobox showing last-updated date
• for GO section, add small note of evidence code and a link to Pubmed reference, if available.
• add image maps to thumbnail expression images so that tissues can be identified
• add a banner from gene talk pages to portal page ([3])

Add/improve stub data (structure)

• add reference to GO section of infobox linking Entrez Gene
• Add a legend to the protein infobox, especially to explain what the expression profiles mean and how they were generated. See User_talk:ProteinBoxBot/Archives/Archive1#Some_comments_and_a_question

Technical bot stuff

• add MCB template to talk page
• Create more precise PDB caption by using the PDB "title"
• Change PDB image name to correspond to the PDB ID, not the gene Symbol
• change images to upload to Wikipedia:Wikimedia Commons
• Mechanism for users to interrupt actions of bot
• replace move expression image captions from image to text (Wikipedia:Preparing images for upload#Replace captions in the image with text)
• add template categories to {{PBB}} templates
• SVG instead of PNG for thumbnail expression images
• tag review articles in "Further reading" section with REVIEW (see User_talk:ProteinBoxBot/Archives/Archive1#Alternative_Idea)
• endash instead of hyphens in references ([4])
• change PDB image link (which currently references only www.pdb.org) to a structure-specific page. Also reference the license agreement (http://www.pdb.org/robohelp_f/site_navigation/citing_the_pdb.htm) (This item may become obsolete with change to EBI images in wikicommons...)
• test out using flare [5] to visualize usage/editing data
• fix duplicate images [6]
• only show 2-3 refs per protein interaction, biasing toward review articles (as discussed here)

Parallel efforts

• upload all PDB to flickr? allows browsing of entire SCOP sub-trees. maybe geotag by location?
• create a WP category for every GO category? (Piggy back with Enzyme class effort?)
• expand to create pages for each disease using {{Infobox_Disease}}
• second bot to wikilink common biology concepts, specifically on pages with PBB_Controls
• change {{Gene}} templates to internal wikilinks
• systematic creation of articles around protein domains (e.g., SMART database)
• Mass autogeneration of high-quality PDB images

Other

• look into HSPA1A and HSPA1B [7]
• automated way to create this table
• create a mac dashboard widget for the Gene Wiki?
• charting library to combine bar chart with background histogram... (not really Gene Wiki related...)

Completed tasks

• Upload snapshots of all PDB images -- create a gallery? Done!
• get structure image from RSCB Done!
  • not sure yet how to get links from genes to PDB entries
  • SCB public domain license is here or here.
• modify orthologs box to automatically adjust rows and columns based on data Done! (I think)...
• possible add a comment to the protein box area saying that changes (to the protein box only) will be overwritten by the next bot update; this may help us from having to worry about manual edits -- AND/OR -- allow users to manually enter comment in protein box to prevent bot from overwriting Done! through the PBB_Controls template.
• use "Category: Human proteins" instead of simply "Proteins" Done!
• add "Category: Gene from chromosome N" Done!
• change spacing pattern (e.g., [8]) Fixed when infoboxes moved to template pages

Obsolete tasks

• second bot to create redirects from gene aliases Removed! better for a human to do
• add a comment <!--Add additional text here--> to make it clear where people can/should edit... Removed! better constrain areas for PBB edits
• changing redirects so that primary title is HGNC name
  • maybe just flag these for manual inspection Removed! A human should handle anything with regards to page moves.
• adding links to page (e.g., "ITK") from alternate symbols (e.g., EMT; LYK; PSCTK2; MGC126257; MGC126258) and full gene name (e.g., IL2-inducible T-cell kinase)
  • is redirecting from alternate symbols really a good idea? How would one list ITK on the EMT disambiguation page? Removed! Better that a human does this.
• add a "update_PDB_image" tag in PBB_controls so that people can turn off automated edits for that part of the infobox specifically -- or, don't make any change to existing PDB image, only add if an image didn't previously exist Removed! Already default behavior