Ontology Notes in BioPortal

BioPortal uses ontology notes to describe a variety of user-specified comments and metadata on ontology, including new-term proposals, proposals for changes, comments and questions about classes, and so on.

Types of notes in BioPortal

The following are the types of notes in BioPortal. Please, email us at support@bioontology.org if you have suggestions for other note types (or specific parameters for the notes).

Basic comments (as they are in BioPortal currently)
Proposals
- New term proposal
  - Generated ID
  - PrefName
  - Synonym
  - Definition
  - Superclass
  - Comment
- New relationship proposal
  - Relationship type: is-a, part-of
  - Relationship target
- New attribute value proposal
  - Attribute: documentation, definition, etc.
  - New value
  - Flag: replaces the current value (which one, in case of multiple values) or in addition to the current value(s)
  - Special kind of new attribute value proposal: Assigning UMLS semantic type
    - Semantic type
    - Semantic typeID

(for later) Structured annotations with user-defined structure
(for later) Usage-guideline notes

Services to access and generate notes

(Note: We are currently working on these services. They are not available yet! If you have specific requirements that the list of services below does not satisfy, please contact us at support@bioontology.org)

Sample of the XML returned for a note

<success>
  <accessedResource>/bioportal/virtual/notes/1104</accessedResource>
  <accessDate>2010-04-26 13:02:57.418 PDT</accessDate>
  <data>
    <list>
      <noteBean>
        <id>Note_0a78922c-3d1e-4689-8af8-48d10d4cdaa8</id>
        <ontologyId>1104</ontologyId>
        <type>Comment</type>
        <author>38143</author>
        <created>1272070868364</created>
        <updated>1272070868250</updated>
        <subject>Including clinical trial data as clinical data</subject>
        <body>I note that clinical data is specifically defined not to include clinical trial data. So is anyone already thinking about where at a high level subtrees might be added to deal with clinical trial data and clinical trial management systems? Or is it premature to do that? This is for the CTSAs.</body>
        <createdInOntologyVersion>2</createdInOntologyVersion>
        <appliesToList>
          <appliesTo>
            <fullId>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Data</fullId>
            <type>Class</type>
          </appliesTo>
        </appliesToList>
      </noteBean>
    </list>
  </data>
</success>

Get notes for an ontology by version id

Signature: ./notes/{ontology version id}?email={email_address}
Description: returns all notes for a specific version of the ontology
Optional arguments:
- noteType={noteType} - returns only the notes of the specific type
- includeArchived=[true|false] - include archived notes; default is false.

Get notes for an ontology by virtual id

Signature: ./virtual/notes/{ontology virtual id}?email={email_address}
Description: returns all notes for the virtual ontology, i.e., all notes associated with any version of this ontology
Optional arguments:
- noteType={noteType} - returns only the notes of the specific type
- includeArchived=[true|false] - include archived notes; default is false.

Get notes for a concept in an ontology by ontology version id

Signature: ./notes/{ontology version id}/{concept id}?email={email_address}
Alt Signature: ./notes/{ontology version id}/?conceptid={uri-encoded concept id}&email={email_address}
Description: returns all notes that are attached to a class in a specific version of the ontology
Optional arguments:
- noteType={noteType} - returns only the notes of the specific type
- includeArchived=[true|false] - include archived notes; default is false.

Get notes for a concept in an ontology by virtual id if the ontology

Signature: ./virtual/notes/{ontology version id}/{concept id}?email={email_address}
Alt Signature: ./virtual/notes/{ontology version id}/?conceptid={uri-encoded concept id}&email={email_address}
Description: returns all notes for a concept in the virtual ontology, i.e., all notes associated with any version of this ontology
Optional arguments:
- noteType={noteType} - returns only the notes of the specific type
- includeArchived=[true|false] - include archived notes; default is false.

Get notes on another note

Signature: ./notes/{note id}?email={email_address}
Description: returns all notes that are attached to a specific note (usually, replies in a discussion)
Optional arguments:
- noteType={noteType} - returns only the notes of the specific type
- includeArchived=[true|false] - include archived notes; default is false.

Create a note for a concept in an ontology (by ontology version id)

Signature: always by ontology version id
Description: creates a note of a specific type with a specific set of values
- create a note, given
  - note type
  - author
  - date
  - appliedTo
  - values
    - relationship-value pairs

Ontology Notes

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