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eVOC Ontologies v2.1

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
  • Treatment
were contributed to eVOC 2.1 by Electric Genetics Pty. Ltd.

Summary of eVOC v2.1

The data mapped was taken from Genbank release 142 (15/06/2004) and includes cumulative updates up until 03/08/2004.

Ontology Numbers of Terms Annotated cDNA Libraries1
Anatomical System 379 7693 (93%)
Associated With 24 0 (0%)3
Cell Type 162 594 (7%)2
Developmental Stage 155 6739 (81%)
Microarray Platform 19 8296 (100%)4
Pathology 171 7024 (85%)
Pooling 8 8092 (98%)
Treatment 24 0 (0%)3

Total number of annotated cDNA libraries: 8296

Notes:

  1. All cDNA libraries are mapped to each ontology but are only considered annotated if they are mapped to terms other than unclassifiable or pending.
  2. Many cDNA libraries are not annotated with specific cell type information and are therefore mapped to unclassifiable.
  3. 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.
  4. cDNA library data is mapped to term not applicable in the Microarray Platform ontology.

Download eVOC v2.1 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 eight 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] (11K)

Annotated Ontologies:

  • eVOC tab-delimited flatfile format [4] (15M)
  • OWL format [5] (731K)
  • HTML format [6] (516K)

File Format Documentation:

  • PDF [7] (100K)
  • Postscript [8] (83K)
  • HTML [9] (17K)

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Page last modified on February 01, 2005, at 02:16 PM
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