Introduction to Annotations

This document is retained for reference purposes for TCGA and should not be considered the current GDC standard. For information on the existing GDC use of annotations please see the Annotations Encyclopedia entry.

This document was adapted from https://wiki.nci.nih.gov/pages/viewpage.action?spaceKey=TCGA&title=Introduction+to+Annotations

This section includes the following topics.

Contents of this page

  • Annotations Overview
  • Annotation Classification and Categories

Annotations Overview

The Annotations application allows authorized TCGA team members to add annotations about TCGA patients and samples down to the aliquot level. These annotations are searchable by the general public, and contain important information about TCGA patients and samples needed for complete and accurate analysis and interpretation of TCGA data. The current general annotation types are: redaction, notification, CenterNotification, and observation. Redactions and notifications are made under BCR authority. Each annotation is categorized using controlled vocabulary. Free-form text notes may also be added. Any TCGA user may search and download annotations against a number of metadata fields.

An annotation has multiple components, described in the following table.

Component Description
Item type Patient, Sample, Portion, Slide, Analyte, Aliquot
Disease Tumor type, by abbreviation
Item Barcode barcode of TCGA item
Item UUID UUID of TCGA item
Annotation Classification controlled vocabulary, see the table below
Annotation Category controlled vocabulary, see the table below
Notes collection of free text notes, can be added to annotations after creation
Other metadata timestamp, creator

The following image shows annotation components in the search results.

search results page

Annotation Classification and Categories

Categories and types of annotations have been explicitly defined, as shown in the following table.

Annotation authority

If an annotation appears, it appears under the authority of a certain component of TCGA. The authorizing group can be determined from the annotation classification. For example, Redactions and Notifications possess Program Office level authority; they are 'official', while Observations are notes from the user base and are 'unofficial'".

Annotation Classification Annotation Category Authority Admissible for Items Usage notes
Redaction Tumor tissue origin incorrect BCR Patient, Sample Use Annotation Note to indicate details, e.g. "Case was of non-ovarian origin"
Redaction Tumor type incorrect BCR Patient, Sample Applies to mislabeling of a disease study, organ or tissue
Redaction Genotype mismatch BCR (Patient+Analyte), (Sample+Analyte) Incorporates conditions such as "Failed SSTR"
Redaction Subject withdrew consent BCR Patient
Redaction Subject identity unknown BCR Patient Applies to patients categorized under the wrong TSS-to-BCR mapping
Redaction Duplicate case BCR Patient Applies to the second (and higher) instance(s) of the same patient being accessioned through TCGA. E.g. "duplicated subject 0981"
Redaction Administrative Compliance BCR Patient Use Annotation Note to indicate details e.g. "Case not meeting regulatory requirements for TCGA"
Notification Prior malignancy BCR Patient
Notification Neoadjuvant therapy BCR Patient
Notification Qualification metrics changed BCR Any
Notification Pathology outside specification BCR Sample, Portion, Slide
Notification Molecular analysis outside specification BCR Sample, Portion, Analyte, Aliquot
Notification Clinical data insufficient BCR Patient
Notification Item does not meet study protocol BCR Any This can be used for infrequently encountered situations (e.g, not Prior malignancy or Neoadjuvant therapy); details should be supplied in an Annotation Note.
Notification Item in special subset BCR Patient, Sample Use to indicate that an item is involved in a "side study". Use free text 'Annotation Note' to indicate study (e.g. "Necrosis study", "Indivumed Prior Malignancy").
Notification Qualified in error BCR Patient
Notification Item is noncanonical BCR Any
Notification New notification type BCR Any
Notification History of unacceptable prior treatment related to a prior/other malignancy BCR Patient
Notification History of acceptable prior treatment related to a prior/other malignancy BCR Patient
Notification Case submitted is found to be a recurrence after submission BCR Patient
Notification Synchronous malignancy BCR Patient
CenterNotification Center QC failed GSC or GCC Patient, Sample, Analyte, Aliquot QC failures at GCC/GSC/GDAC level, note describes the issue
CenterNotification Item flagged DNU GSC or GCC Patient, Sample, Analyte, Aliquot "Do not use" flag, applied by GCC/GSC/GDAC
Observation Tumor class but appears normal Authorized User Sample, Portion, Slide, Analyte, Aliquot
Observation Normal class but appears diseased Authorized User Sample, Portion, Slide, Analyte, Aliquot
Observation Item may not meet study protocol Authorized User Any
Observation General Authorized User Any
Observation New observation type Authorized User Any user-suggested observation type