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eVOC Ontologies v2.5

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Recent Changes to eVOC

eVOC 2.5 saw a relatively large number of term additions, move and name changes. These are listed below:

  • Anatomical System:
    • Term additions:
      • "palatine tonsil" added as a child of "tonsil".
      • "blastocyst" added as a child of "female reproductive system".
      • "blastocyst inner cell mass" added as a child of "blastocyst".
    • Term moves:
      • "trophoblast" moved to be a child of "blastocyst". It was a child of "female genitals" (now "female reproductive system").
    • Term name changes:
      • "alimentary" replaced by "alimentary system".
      • "cardiovascular" replaced by "cardiovascular system".
      • "dermal" replaced by "dermal system".
      • "developmental" replaced by "developmental anatomy".
      • "endocrine" replaced by "endocrine system".
      • "haematological" replaced by "hematological system".
      • "lymphoreticular" replaced by "lymphoreticular system".
      • "musculoskeletal" replaced by "musculoskeletal system".
      • "nervous" replaced by "nervous system".
      • "respiratory" replaced by "respiratory system".
      • "genital" replaced by "reproductive system"
      • "urogenital" replaced by "urogenital system".
      • "female genitals" replaced by "female reproductive system".
      • "male genitals" replaced by "male reproductive system".
      • "urinary" replaced by "urinary system".
    • Synonyms changes:
      • "digestive" replaced by "digestive system".
      • "vascular" replaced by "vascular system".
      • "genitourinary" replaced by "genitourinary system".

  • Cell Type:
    • Term name changes:
      • "epithelium" replaced by "epithelial cell".

  • Pathology:
    • Terms additions:
      • "acute myelogenous leukemia" added as a child of "myeloid leukemia". Added with the synonyms "AML" and "acute myeloid leukemia".
      • "keratoconus" added as a child of "other disorders".
    • Term name changes:
      • "Hodgkin's" replaced by "Hodgkin's lymphoma".
      • "non-Hodgkin's" replaced by "non-Hodgkin's lymphoma".
      • "Burkitt's" replaced by "Burkitt's lymphoma".
      • "myeloid" replaced "myeloid leukemia".
    • Synonyms changes:
      • Synonym "AML" removed from term "monocytic".
      • Synonyms "CML", "chronic myeloid leukemia" and 
            "chronic granulocytic leukemia" added to
            term "chronic myelogenous leukemia".

Summary of eVOC v2.5

The data mapped was taken from Genbank release 144 (October 15, 2004) and includes cumulative updates up until November 30, 2004.

Ontology Numbers of Terms Annotated cDNA Libraries1
Anatomical System 396 7837 (93%)
Associated With 24 0 (0%)3
Cell Type 166 656 (8%)2
Developmental Stage 155 6831 (81%)
Experimental Technique 28 8392 (100%)
Microarray Platform 19 8392 (100%)4
Pathology 178 7088 (84%)
Pooling 9 8153 (97%)
Tissue Preparation 8 6967 (83%)
Treatment 24 0 (0%)3

Total number of annotated cDNA libraries: 8392

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 v2.5 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] (18K)
  • GO flatfile format [2] (11K)
  • OBO file format [3] (13K)

Annotated Ontologies:

  • eVOC tab-delimited flatfile format [4] (707K)1
  • OWL format [5] (935K)
  • HTML format [6] (646K)

File Format Documentation:

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

Notes:

  1. The eVOC tab-delimited flatfile used to include the data file containing the EST to cDNA mappings. This file is now available on the data download page and so is not included here.

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Page last modified on February 14, 2005, at 01:52 PM
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