1. Insight into GO and GOA Angelica Tulipano , INFN Bari CNR
Giulia De Sario , ITB Bari CNR
Andreas Gisel, ITB Bari CNR
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov -9.Nov 2007

2. GODB GO_200709 3,3 million gene products more than 100000 organisms
The GO Database, which comprises both ontology and annotation data, is built from the flat files available on the GO website, and can be downloaded in mySQL or RDF XML format.
termdb
ontologies, definitions and mappings to other dbs
assocdb
the above, plus associations to gene products
seqdb
the above, plus protein sequences for some of the gene products
seqdblite
the above, with IEA associations stripped out (this is the version that drives AmiGO)
GO_200709
3,3 million gene products
more than organisms
25000 GO terms
14,5 million associations
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

3. GO tree - path Total terms 24955
Number of terms without child (60%)
Number of terms with children (40%)
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

4. GO tree - path Total terms 24955 Number of terms without child 14974
Number of terms with children
Number of different path
Average number of path / end term 17
Max number of path / end term 851
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

5. GO tree - path Total terms 24955 Number of terms without child 14974
Number of terms with children
Average length of path 10
Max length of path 18
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

6. GO tree - path
The GO is very wide and has a large knowledge to associate with gene products,
however the depth of the path is quite short
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

7. Gene product description
BCL2_HUMAN
3 million gene products (UniProt) are described by descriptions
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

8. Gene product description
BCL2_HUMAN
GODB version go_09_07
Gene product
per description Descriptions Gene products
3 million gene products (UniProt) described by descriptions
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

9. GOA Evidence Description Code Inferred by Curator IC experimental
Inferred from Direct Assay IDA experimental
Inferred from Electronic Annotation IEA computational
Inferred from Expression Pattern IEP experimental
Inferred from Genetic Interaction IGI experimental
Inferred from Mutant Phenotype IMP experimental
Inferred from Physical Interaction IPI experimental
Inferred from Sequence or Structural Similarity ISS computational
Non-traceable Author Statement NAS experimental
No biological Data available ND --
Inferred from Reviewed Computational Analysis RCA computational
Traceable Author Statement TAS experimental
Not Recorded NR --
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

10. GOA Evidence Description Code Inferred by Curator IC exp 388
Inferred from Direct Assay IDA exp 10888
Inferred from Electronic Annotation IEA comp ,5%
Inferred from Expression Pattern IEP exp 392
Inferred from Genetic Interaction IGI exp 145
Inferred from Mutant Phenotype IMP exp 1646
Inferred from Physical Interaction IPI exp 7517
Inferred from Sequence or Structural Similarity ISS comp 16759
Non-traceable Author Statement NAS exp 10811
No biological Data available ND
Inferred from Reviewed Computational Analysis RCA comp 107
Traceable Author Statement TAS exp 19463
Not Recorded NR
total associations %
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

11. GOA p-value
The number of gene products associated to a term or any of its children, divided by the number of total associations between the GO terms and gene products.
The smaller the p(term) is the higher the information content and the more detailed the description.
name level term-type count p(term)
molecular_function 1 molecular_function
biological_process 1 biological_process
cellular_component 1 cellular_component
hormone activity 4 molecular_function
Gliogenesis 4 biological_process e-05
cell fate specification 5 biological_process e-05
Angiogenesis 7 biological_process e-05
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

12. GOA delta p-value
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

13. GOA p-value
One would expect a linear increase of the information content along a path
Re-evaluate annotaions and GO term choise according such studies
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007

14. GO - GOA
Important knowledge to understand better biological data
Urgent need to collect and incoorporate existent information especially from non-model organisms
THANKS!!!!!!
EMBRACE Workshop on ‘Applied Gene Ontology’ Bari, Italy 7.Nov - 9.Nov 2007