Talk:BioWiki

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Contents 1 Results table 2 BioWiki pages 3 Migration 4 TODO 5 Wiki activity script 6 BioWiki demo queries 6.1 BioWiki page modification date query 6.2 BioWiki API URL query 7 Try a query... 8 Try a category tree

Results table

The results table on the BioWiki page is generated using the SMW 'tabular output' recipe at http://smw.referata.com. The table uses the following components:

• Template:BioWiki/Table_header
• Template:BioWiki/Table_body
• Template:BioWiki/Table_footer

If you want to change the table layout, you will have to edit all three templates together with the query (on the BioWiki page). IDE anyone?

BioWiki pages

The BioWiki pages are generated and edited using the 'BioWiki form', which is simply a (data and data type aware) template editor. It edits calls to the 'BioWiki template'. The template itself formats and annotates the data passed in the template call. Again, changing the structure of the data requires editing both the form and the template together, ensuring that all BioWiki pages carry the correct template.

For quick reference:

• BioWiki form
• BioWiki template
• BioWiki pages here or of course here.

Migration

The site was migrated from a temporary location using the following Perl scripts to interface the MediaWiki::API:

• BioWiki/migrate_biowiki_pages.plx
• BioWiki/migrate_biowiki_logos.plx

TODO

• The BioWiki data
  • Set up a cron job to run the activity monitor script.
  • Add a field to estimate the size of the target community.
  • Check the contact email for each wiki.

• Interface
  • It feels like there should be an [edit] on the right hand side somewhere - people are used to that appearing to the right of section headers.
  • The link back from a BioWiki page to the BioWiki table is hard to find.

• Bonus
  • Build a 'score' for ranking complete entries. Should be easy enough using #if's.
  • Switch Links and References formedit links to the new floatedit type.

Wiki activity script

Here is the first working prototype for the wiki activity script.

The working script is now available here: https://github.com/dbolser/BioWiki

BioWiki demo queries

BioWiki page modification date query

Useful for debugging:

Recently modified BioWikis 

SubtiWiki, Sajun.Org, SNPedia, SEQwiki, PyMOLWiki … further results

Least recently modified BioWikis 

Bioinformatist.org, Topsan, Proteopedia, MetaBase, WikiGenes … further results

BioWiki API URL query

	MediaWiki API URL
Bio2RDF	http://sourceforge.net/apps/mediawiki/bio2rdf/api.php
BioFoundation.Net	http://biofoundation.net/api.php
BioPedia	http://biopedia.org/api.php
BioPerl Wiki	http://www.bioperl.org/w/api.php
Biocompany.net	http://biocompany.net/api.php
… further results

CSV

Try a query...

Bio2RDF, BioFoundation.Net, BioPedia, BioPerl Wiki, Biocompany.net, Bioinformatics.Org Wiki, Bioinformatist.org, Biomatics.Org, Biopeople.org, Biosophy.org, Biowiki.net, Brede Wiki, Bvio, CCP4 users' wiki, CHDWiki, ConceptWiki.org, DrugMet, EcoliWiki, GMOD Wiki, GONUTS, Gene Ontology Consortium Wiki, Gene Wiki, Genomics.Org, Jmol Wiki, MetaBase, Metagenes, MyBio, NeuroLex, NeuroWiki, Omics.org, OpenWetWare, PDBWiki, Proteopedia, PyMOLWiki, SEQwiki, SNPedia, Sajun.Org, SubtiWiki, SubtilisWiki, TFe, Topsan, WikiGenes, WikiPathways, WikiProject RNA, XDSwiki, Xenopus Wiki

46

Try a category tree

No value

• Sandbox:Person a (Knows Sandbox:Person b)
• Sandbox:Person b (Knows Sandbox:Person c, Sandbox:Person a)
• Sandbox:Person c (Knows Sandbox:Person a)