587:
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
714:
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
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UniProt fields: PFAM, "Protein name", "Synonyms", FUNCTION, DOMAIN, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, and WEB RESOURCE
76:
52:
425:
change PDB image link (which currently references only www.pdb.org) to a structure-specific page. Also reference the license agreement (
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352:
Add a legend to the protein infobox, especially to explain what the expression profiles mean and how they were generated. See
235:
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31:: This page is effectively read-only, except by the bot organizers. Please post any ideas and suggestions on the
703:
is redirecting from alternate symbols really a good idea? How would one list ITK on the EMT disambiguation page?
32:
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310:(need to either change default in template, or need to do a second pass run on all infoboxes to add parameter)
535:
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524:
charting library to combine bar chart with background histogram... (not really Gene Wiki related...)
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add a comment <!--Add additional text here--> to make it clear where people can/should edit...
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47:: The items below are thoughts for the future and are not included in the initial proposed specs.
17:
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upload all PDB to flickr? allows browsing of entire SCOP sub-trees. maybe geotag by location?
322:
for GO section, add small note of evidence code and a link to Pubmed reference, if available.
681:
333:
118:
677:
443:
only show 2-3 refs per protein interaction, biasing toward review articles (as discussed
157:
figure out synchronization with wikidraft.org/SMW, converting SWLs to real semantic links
178:
retrieve MeSH terms identify matching species (human, mouse, zebrafish, fly, rat, yeast)
507:
475:
second bot to wikilink common biology concepts, specifically on pages with PBB_Controls
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460:
create a WP category for every GO category? (Piggy back with Enzyme class effort?)
385:
Knowledge (XXG):Preparing images for upload#Replace captions in the image with text
491:
systematic creation of articles around protein domains (e.g., SMART database)
429:) (This item may become obsolete with change to EBI images in wikicommons...)
326:
578:
modify orthologs box to automatically adjust rows and columns based on data
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294:
import and display protein domain information (through
Uniprot/PFAM/COGs)
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change format of the references section to make it small-screen friendly (
263:
KEGG (also add wikilinks to other gene pages in the same KEGG pathways)
225:
for articles that reference a pub multiple times, concatenate sentences
433:
371:
Change PDB image name to correspond to the PDB ID, not the gene Symbol
354:
User_talk:ProteinBoxBot/Archives/Archive1#Some_comments_and_a_question
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User_talk:ProteinBoxBot#Mouse_location_links_lack_db_name_parameter
427:
http://www.pdb.org/robohelp_f/site_navigation/citing_the_pdb.htm
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to thumbnail expression images so that tissues can be identified
169:
673:
669:
315:
User_talk:ProteinBoxBot/Archives/Archive1#Interaction_partners
222:
for pubs that reference multiple species, one line per species
219:
is there a MeSH-to-taxonomy mapping? or do free-text matching?
597:
use "Category: Human proteins" instead of simply "Proteins"
383:
replace move expression image captions from image to text (
662:
A human should handle anything with regards to page moves.
414:
User_talk:ProteinBoxBot/Archives/Archive1#Alternative_Idea
349:
add reference to GO section of infobox linking Entrez Gene
368:
Create more precise PDB caption by using the PDB "title"
160:
OUTPUT: demonstrate real inline queries on wikidraft.org
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not sure yet how to get links from genes to PDB entries
512:
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650:
changing redirects so that primary title is HGNC name
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tag review articles in "Further reading" section with
175:
scan through all Gene Wiki pages for inline citations
403:SVG instead of PNG for thumbnail expression images
632:second bot to create redirects from gene aliases
380:Mechanism for users to interrupt actions of bot
319:Add a note in infobox showing last-updated date
495:Mass autogeneration of high-quality PDB images
463:expand to create pages for each disease using
304:Need to fix the db links for genome locations
234:redesign infobox to better handle linking to
67:, add PDB infobox to all PDB images (Example
8:
168:pilot collaboration with MODs (specifically
657:maybe just flag these for manual inspection
419:endash instead of hyphens in references (
238:(MGD, RGD, ZFIN, FlyBase, WormBase, etc.)
288:Add GeneRIFs and references from Uniprot
77:needs to work with new data Web services
203:sentence(s) referencing the publication
145:encode them in Gene Wiki article using
621:when infoboxes moved to template pages
605:add "Category: Gene from chromosome N"
332:add a banner from gene talk pages to
277:Add/improve stub data (gene-specific)
7:
646:better constrain areas for PBB edits
306:: default for mouse has gone to mm9
272:-- would need community consensus...
53:User:ProteinBoxBot/Project_proposals
593:through the PBB_Controls template.
536:Upload snapshots of all PDB images
24:
672:") from alternate symbols (e.g.,
376:Knowledge (XXG):Wikimedia Commons
344:Add/improve stub data (structure)
181:generate four-column output file:
39:Development plan and future ideas
270:link to Bioinformatic Harvester?
488:templates to internal wikilinks
435:to visualize usage/editing data
708:Better that a human does this.
613:change spacing pattern (e.g.,
163:OUTPUT: export from SMW to RDF
114:templates can use the generic
1:
668:adding links to page (e.g., "
563:SCB public domain license is
550:get structure image from RSCB
365:add MCB template to talk page
692:) and full gene name (e.g.,
506:look into HSPA1A and HSPA1B
291:import and display EC number
694:IL2-inducible T-cell kinase
390:add template categories to
374:change images to upload to
735:
313:Load PPI from Entrez Gene
200:matching organisms by MeSH
142:find some well-known facts
58:Next up for implementation
720:Already default behavior
637:better for a human to do
511:automated way to create
296:See previous discussion.
438:fix duplicate images
432:test out using flare
65:discussion on Commons
519:mac dashboard widget
243:Add additional links
101:from main namespace
360:Technical bot stuff
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521:for the Gene Wiki?
130:pilot project for
104:blocking edits to
18:User:ProteinBoxBot
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452:Parallel efforts
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254:wikiprofessional
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529:Completed tasks
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468:Infobox_Disease
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197:cited pubmed ID
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73:Run bot update
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583:(I think)...
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538:-- create a
486:}}
480:{{
471:}}
465:{{
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398:}}
392:{{
303:
251:nextbio.com?
153:}}
147:{{
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132:{{
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116:{{
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106:{{
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96:PBB_Controls
93:{{
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83:{{
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26:
25:
588:overwriting
334:portal page
86:PBB_Summary
513:this table
327:image maps
51:See also:
690:MGC126258
686:MGC126257
517:create a
400:templates
257:wikigenes
248:GeneCards
718:Removed!
706:Removed!
660:Removed!
644:Removed!
635:Removed!
540:gallery
478:change
81:remove
682:PSCTK2
409:REVIEW
119:nobots
715:exist
619:Fixed
608:Done!
600:Done!
591:Done!
581:Done!
553:Done!
545:Done!
501:Other
412:(see
212:Notes
16:<
569:here
565:here
483:Gene
445:here
325:add
266:HPRD
236:MODs
170:ZFIN
91:and
63:per
45:NOTE
28:NOTE
678:LYK
674:EMT
670:ITK
567:or
395:PBB
150:SWL
135:SWL
109:PBB
696:)
688:;
684:;
680:;
676:;
172:)
35:.
616:)
571:.
542:?
447:)
422:)
416:)
387:)
339:)
336:(
285:)
70:)
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
