From GO Public
Some ideas for Minimum standards for GO tools:
- 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)
- 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]