OBI Adding New Term Policy

To add a new term into OBI, please provide minimal required metadata of the term if possible, which are 

 Definition
 Definition Source
 Definition Editor
 Editor Preferred Term
 Curation status

 the genus-species form: An A =def. a B which Cs, where B is the parent of the defined term A and C is the defining characteristic of those Bs which are also As.

For example, the textual definition of OBI_'container' (a subclass of 'device') is: 

 A device that can be used to restrict the location of material entities over time.

For a defined class, which could have more than one parent class after reasoning. The definition is not necessary to begin with its direct superclass. It can start with 'a material entity' (subclass of '_defined_material') or 'a processual_entity' (subclass of '_defined processes'). For example, the textual definition of OBI_'specimen' (a subclass of '_defined_material') is: 

 A material entity that has the specimen role.
  • Definition Editor: to distinguish the editor is a person or a group. The 'PERSON:' or 'GROUP:' will be added and followed by person name(s) or group name(s), respectively. The 'PERSON:' or 'GROUP:' are case insensitive. For example, 
 PERSON:Bjoern Peters
 Group:OBI group

If there are multiple editors, it can create Definition Editor annotation for each person/group, or using comma separate different persons/groups in one Definition Editor annotation. For example, 

 Definition Editor - PERSON:Bjoern Peters,Helen Parkinson

or 

 Definition Editor - PERSON:Bjoern Peters
 Definition Editor - PERSON:Helen Parkinson

Both formats are fine.

  • Definition Source: could be person(s), group, website, external ontology, ISBN, PUBMED ID, DOI, etc. For example, 
 PERSON:Chris Stoeckert
 GROUP:OBI group
 WEB:http://en.wikipedia.org/wiki/Microarray
 MO_697 arrayer

If definition is taken or modified from an external ontology term, it is recommended provide the external ontology term ID.

  • Editor Preferred Term: should be same as the term label

The Term Label will be copied to 'Editor Preferred Term' using the script during the OBI release. It means any value given in this annotation will be overwritten. It is recommended 

 not touch this annotation when you add/edit terms

If you would like to add synonym, please add it to 'alternative term'.

  • curation status: commonly used curation status when adding a new term: 
 uncurated: nothing except label
 metadata incomplete: not all required metadata are provided or the editor still works on the provided minimal metadata. (should be more than label provided)
 metadata complete: all required metadata have been provided

It is not recommended set the curation status of a term as 'pending final vetting' and 'ready for release' if nobody other than the definition editor which is one person review the term.

In the OBI release version, no term should be at 'uncurated' status. The terms which curation status is 'organizational term' (renamed from 'placeholder') or 'example to be eventually removed' will be removed before the release.

Details of OBI metadata and the allowed values of curation status, please check: http://obi-ontology.org/page/OBI_Minimal_metadata

(Discussed and approved on Aug 30, 2010 dev call)

Retrieved from "http://www.obi-ontology.org/page/OBI_Adding_New_Term_Policy"

Search

Tools

This page