This is a WORK IN PROGRESS but will provide guidelines on the usage of biotoolsSchema for annotating bioinformatics software resources, particularly for registration in the bio.tools registry.
IMPORTANT these are very rough notes and describe in places future plans.
Basic details that will be included:
- Semantics of resource / interface type (consider consolidated into a single, inuititive set)
- Text from schema
- Facets and patterns
- Enumerations
- Samples (but improve these by using real world examples)
General guidelines are given below.
The guidelines will cover:
- Format of resource ID in bio.tools (version is optional)
- bio.tools/toolName/version
- bio.tools/serviceProviderName/serviceName/version
- how IDs are created
- persistence of corresponding tool pages
- implications of changing toolName, serviceProviderName, serviceName, version
The guidelines will describe how bio.tools entries can / should / must be related to one another:
- Tool isNewVersionOf Tool
- Tool isOldVersionOf Tool
- Service usesAsDataSource Database
- Service uses Tool
- Platform includes Tool
- Platform includes Service
- Platform includes Database
- Container includes Tool
- Container includes Service
- Container includes Database
And maybe
- Workflow uses Tool
- Workflow uses Service
- Workflow uses Database
Below are guidelines for different elements (fields of information) defined by the biotoolsSchema XSD schema.
- Describe the ID URL pattern used by bio.tools:
- bio.tools/toolName/version
- bio.tools/serviceProviderName/serviceName/
- bio.tools/database/databaseName/
- "toolName" is identical to (see below)
- "serviceProviderName" is specified upon registration (how?) and is identical to bio.tools subdomain (if the registrant wants this). The value is normally the standard acronym (e.g. EMBL-EBI) or short form name of the institute.
- "version" may be specified for tools only. It is optional and is identical to (see below).
-
Describe the facet and regex in English.
-
What to do if the unique name has been taken.
-
Stress this is used in the resource ID - and the implications of changing it.
-
What to do for tools that do not have an obvious homepage (with an example of such).
- Style guidelines - what this should / should not normally contain.
- Include table explaining the enum, with examples of each type!
- Explaim cases where more than 1 resource type could apply (e.g. a database, that provides an API and various Web apps), and that all types should be specified in such cases.
- Describe the facet and regex in English.
- Stress this will be used in the resource ID (if specified) and the implications of changing it.
Below are guidelines for the different types of resources that may be registered in the bio.tools registry.