Qualitative Data
Annotations to describe the amount of transcript/protein level or the changes in level which occur in different conditions or at different phases in WT cells.
- Qualitative Expression annotation comprises of 5 pieces of data: Expression Type, Annotation extension( Relation), Level, Evidence and reference
- Qualitative expression is currently curated in Artemis, but will eventually be captured in Canto
- Syntax
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:xxxxxxx); qualifier=increased; evidence=ECO:xxxx; db_xref=PMID:xxxxxxx; date=YYYYMMDD"
Expression Type
| Allowed Type | Comment
|
| RNA level | A northern blot (for instance) can only tell you if there is RNA there
|
| protein level | -
|
| transcription | Requires a specific assay for transcription, not only presence of RNA, as could be decreased degradation
|
| RNA degradation | Requiers a specific assay for degradation
|
| translation | -
|
| protein degradation | -
|
Annotation extension (Relation)
| Allowed relations | Syntax (Example) | comment
|
| during | during(GO biological process ID) | Commonly vegetative growth (ID)
|
| in_presence_of | In_presence_of(ChEBI ID) | -
|
| occurs_in | (cell type) | -
|
- Unstressed conditions include during "vegetative growth of single-celled organism" (=whole cell extract) or "mitotic/meiotic cell cycle" (= they looked at different phases))
- Unstressed conditions include growth on YE and MM unless there is a known difference between the two (in which case EMM might eg be a starvation condition
Level
- allowed qualifiers: present, absent, unchanged, increased, decreased, constant, fluctuates
Evidence
| Evidence codes
|
| ECO:0000112 | Western blot assay
|
| ECO:0000106 | Northern assay evidence
|
| ECO:0000049 | reporter gene assay
|
| ECO:0000108 | RT-PCR (reverse transcriptase)
|
| ECO:0000110 | RNA protection assay evidence
|
| ECO:0000058 | expression microarray evidence
|
| ECO:0000231 | qPCR / (quantitative / real time pcr)
|
| ECO:0000124 | fusion protein localization evidence
|
| ECO:0000007 | immunofluorescence
|
| Examples
|
| type | relation | level | description | formal
|
| RNA level | during(veg growth) | present | RNA detected during vegetative growth | term=gene expression, RNA level; annotation_extension=during(GO:0072690); qualifier=present; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD"
|
| RNA level | during(cell response to UV | increased | RNA amount increased during UV stress | term=gene expression, RNA level; annotation_extension=during(GO:0034644); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD"
|
| protein level | during(cell response to UV | unchanged | protein level does not change during UV stress compared to unstressed | term=gene expression, protein level; annotation_extension=during(GO:0034644); qualifier=unchanged; evidence=ECO:0000112; db_xref=PMID:1; date=YYYYMMDD"
|
| transcription | during(meiosis) | increased | transcription is increased during meiosis (as opposed to decreased degradation) | term=gene expression, transcription; annotation_extension=during(GO:0007126); qualifier=increased; evidence=ECO:0000108; db_xref=PMID:1; date=YYYYMMDD"
|
Quantitative Data
| Column | Content | Required | Cardinality | Example
|
| 1. | Systematic ID | required | 1 | SPBC11B10.09
|
| 2. | Type | required | 1 | RNA OR protein
|
| 3. | During* | required | 1 | GO:0072690
|
| 4. | Average copies per cell | required | 1 | 5
|
| 5. | Range (of copies/cell) | optional | 1 | 5-10
|
| 6. | Evidence | required | 1 | ECO:0000046
|
| 7. | Qualifier | required | 1 | "population wide" OR " "single cell"
|
| 8. | Source | required | 1 | PMID:12345678
|
- will be converted to annotation_extension=during(GO:0072690)
A property value that captures whether the expression is determined at the level of a single cell or a population. Related but not identical to evidence (some kinds of evidence
allow inferences about expression in an individual cell, whereas other evidence types only support population-level inferences). Property name is "qual_gene_ex_cell_distribution"; value can be "population wide" or "single cell".
