Tools standards

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[edit] Some ideas for Minimum standards for GO tools:

[edit] 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)

[edit] 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)

[edit] 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.


[edit] New Tools Spec

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

# REQUIRED, scalars
name => string,
url => url,
email => email addr,
description => some text,
submission_date => date,	

# REQUIRED, lists
feature => [ one or more from 'ont_view', 'annot_view', 'ont_edit', 'annot_edit', 'stat', 'sw', 'textmine', 'data', 'other' ],
developer => [ array of developers involved, with a database / organization name and URL for each ],

# booleans
is_online_tool => true,  # omit if not true
is_standalone_tool => true,
is_open_source => true,

# optional stuff
publication => [ array of PMID or DOI ids ],
compatible_os => [ one or more of 'windoze', 'mac', 'linux', 'unix'],
Retrieved from "http://wiki.geneontology.org/index.php/Tools_standards"
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