Tools standards

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Some ideas for Minimum standards for GO tools:

Essential:

  • Takes into account tree
  • Considers evidence codes
  • Considers NOT annotations
  • Provides details of version of GO used (how do they indicate this?)
  • Provides details of annotation set used (how do they indicate this?)
  • Update frequency minimum, monthly?
  • Actively maintained/developed
  • Provides good documentation
  • Reproducible (for any tool that performs some analysis)

Desirable:

  • Available for all platforms
  • Development/working group
  • Free to academics
  • Open source
  • Has associated publication
  • Takes into account different relations
  • Works off current live AmiGO release (eg through a mirror)

List of things to ask people when finding out about their tools:

Tool name
URL for the tool
Name and URL of the organization that produced the tool
A contact name and email address for the tool
Tool type or features (pick all that apply):
 browser/search/visualisation
  ontology browser/search
  annotation browser/search
 editor
  ontology editor
  annotation editor
 database
  data warehouse
 analysis
  statistical analysis
   term enrichment
  text mining
 software library
  R library
  Perl library
  Java library
  Other library (specify)
 other (please specify)
Brief description of tool
GO data used:
 GO ontology data
  relationships, tree structure
  synonyms, definitions, comments
 GO annotation data
  evidence codes
  reference data
  qualifier column (NOT, contributes to, ---)
  taxon
Source of GO data
Frequency of GO data update
  • Is the tool web-based or standalone?
  • If the tool is standalone, which platforms can use it? (Windows / Mac / Unix / Linux / other)?
  • Is the tool free to academics?
  • Is the tool open source?
  • Any associated publications (please give PubMed ID if available)
  • Note: we will maintain an archive of previously listed tools, linked from the tools page.


New Tools Spec

This is the current (i.e. in development) incarnation of the tools spec.

tool_name => # tool name
tool_url => # tool URL
organization => # organization(s) that produced the tool
organization_url => # organization URL(s)
contactname => # contact person for the tool
contactemail => # contact e-mail address
tool_type => # tool type or features; one or more of [ "browser", "search", "visualization", "editor", "database", "software", "statistical", "term_enrichment", "text_mining", "other_analysis"
tool_type_other => # other tool feature(s) [optional]
description => # tool description
free => # tool cost; only allowable value is 'true'
open_source => # is the tool open source? allowable values => ['yes', 'no']
platform =># compatible platforms; one or more of ( web win mac unix linux )
publications => # publications; PMIDs or DOIs preferred
go_data => # GO data used; one or more of ( term def syn xref rel gp ev_code ref qual taxon )
go_data_other => # other GO data used [optional]
go_data_src => # GO data source, one or more of ( obo gaf db owl xml other )
go_data_src_other =># other GO data source [optional]
update_frequency => # data update frequency; allowable values are ( daily weekly monthly quarterly no_fixed ) 
comments => # comments [optional]