eVOC Ontologies v2.3
Contents
Recent Changes to eVOC
eVOC was until recently composed of five ontologies:
- Anatomical System
- Pathology
- Developmental Stage
- Cell Type
- Pooling
Three new ontologies
- Associated With,
- Microarray Platform and
- Treatment
were contributed to eVOC 2.1 by Electric Genetics Pty. Ltd.
A further two ontologies
- Tissue Preparation and
- Experimental Technique,
contributed by Gregory Theiler of the Swiss Institute of
Bioninformatics/Ludwig Institute for Cancer Research together with the eVOC team at SANBI, were added to the 2.2 release.
Summary of eVOC v2.3
The data mapped was taken from Genbank release 143 (15/08/2004) and includes cumulative updates up until 03/10/2004.
| Ontology | Numbers of Terms | Annotated cDNA Libraries1 |
|---|
| Anatomical System | 391 | 7831 (93%) |
| Associated With | 24 | 0 (0%)3 |
| Cell Type | 162 | 652 (8%)2 |
| Developmental Stage | 155 | 6825 (81%) |
| Experimental Technique | 28 | 8386 (100%) |
| Microarray Platform | 19 | 8386 (100%)4 |
| Pathology | 174 | 7086 (84%) |
| Pooling | 8 | 8148 (97%) |
| Tissue Preparation | 8 | 6963 (83%) |
| Treatment | 24 | 0 (0%)3 |
Total number of annotated cDNA libraries:
8386
Notes:
- All cDNA libraries are mapped to each ontology but are only considered annotated if they are mapped to terms other than unclassifiable or pending.
- Many cDNA libraries are not annotated with specific cell type information and are therefore mapped to unclassifiable.
- Mapping of the cDNA libraries to the Associated With and Treatment ontologies is work currently being undertaken by the Electric Genetics Evoke team - the unannotated cDNA libraries are associated with the term pending in these two ontologies.
- cDNA library data is mapped to term not applicable in the Microarray Platform ontology.
Download eVOC v2.3 Ontologies
Two flavours of the eVOC ontologies are available for download - annotated and unannotated. The annotated versions list the cDNAs annotated to each term. The unannotated versions contain just the ontology terms. Each download contains all ten ontologies.
All the
available data sets (ESTs, Unigene clusters, H-inv clusters, etc) are mapped to the ontology terms via the cDNAs. Thus if you're downloading data you probably want to get an annotated copy of the ontologies (otherwise you won't be able to connect the data to the ontology terms).
If you're wanting to view the ontologies in
DagEdit you'll need the GO or OBO format. Unfortunately neither of these formats currently support annotations.
If you have
Protege and its OWL plugin, you can download the OWL versions of the ontologies which do contain the cDNA annotations. You can also use the OWL version in
COBrA.
Ontologies:
- eVOC tab-delimited flatfile format [1] (9K)
- GO flatfile format [2] (10K)
- OBO file format [3] (12K)
Annotated Ontologies:
- eVOC tab-delimited flatfile format [4] (16M)1
- OWL format [5] (932K)
- HTML format [6] (644K)
File Format Documentation:
- PDF [7] (100K)
- Postscript [8] (83K)
- HTML [9] (17K)
Notes:
- The eVOC tab-delimited flatfile still includes the data file containing the EST to cDNA mappings. This file is now also available on the data download page. It is probable that in later releases this mapping file will only be found of the data download page (just to keep all the data in one place).
