Tools standards
From GO Public
Contents |
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.
# 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'],
