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PMID:17208035

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Citation

Thomas, PD, Mi, H and Lewis, S (2007) Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol 11:4-11

Abstract

With numerous whole genomes now in hand, and experimental data about genes and biological pathways on the increase, a systems approach to biological research is becoming essential. Ontologies provide a formal representation of knowledge that is amenable to computational as well as human analysis, an obvious underpinning of systems biology. Mapping function to gene products in the genome consists of two, somewhat intertwined enterprises: ontology building and ontology annotation. Ontology building is the formal representation of a domain of knowledge; ontology annotation is association of specific genomic regions (which we refer to simply as 'genes', including genes and their regulatory elements and products such as proteins and functional RNAs) to parts of the ontology. We consider two complementary representations of gene function: the Gene Ontology (GO) and pathway ontologies. GO represents function from the gene's eye view, in relation to a large and growing context of biological knowledge at all levels. Pathway ontologies represent function from the point of view of biochemical reactions and interactions, which are ordered into networks and causal cascades. The more mature GO provides an example of ontology annotation: how conclusions from the scientific literature and from evolutionary relationships are converted into formal statements about gene function. Annotations are made using a variety of different types of evidence, which can be used to estimate the relative reliability of different annotations.

Links

PubMed Online version:10.1016/j.cbpa.2006.11.039

Keywords

Animals; Chromosome Mapping; Computational Biology; Databases, Genetic; Gene Expression Profiling; Genome; Humans; Information Storage and Retrieval/methods; Software

edit table

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

PTHR11361:AN27

GO:0000794: condensed nuclear chromosome

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=1329021
TAIR=locus=2092404

C

Seeded From PANTHER


PTHR11361:AN27

GO:0007129: synapsis

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=1329021
TAIR=locus=2092404

P

Seeded From PANTHER


PTHR11361:AN27

GO:0007131: reciprocal meiotic recombination

ISS: Inferred from Sequence or Structural Similarity: SGD:S000002313
TAIR=locus=2092404

P

Seeded From PANTHER


PTHR11361:AN225

GO:0000794: condensed nuclear chromosome

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=1860077
TAIR=locus=2130913

C

Seeded From PANTHER


PTHR11361:AN225

GO:0007129: synapsis

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=1860077
TAIR=locus=2130913

P

Seeded From PANTHER


PTHR11361:AN26

GO:0000794: condensed nuclear chromosome

ISS: Inferred from Sequence or Structural Similarity: TAIR=locus=2092404
MGI=MGI=1329021
TAIR=locus=2130913
MGI=MGI=1860077

C

Seeded From PANTHER


PTHR11361:AN26

GO:0003006: reproductive developmental process

ISS: Inferred from Sequence or Structural Similarity: SGD:S000005450
GeneDB_Spombe:SPBC19G7.01c
MGI=MGI=101816
MGI=MGI=1860077
SGD:S000000688
GeneDB_Spombe:SPAC8F11.03

P

Seeded From PANTHER


PTHR11361:AN26

GO:0003684: damaged DNA binding

ISS: Inferred from Sequence or Structural Similarity: TAIR=locus=2132233
MGI=MGI=1343961
ENSEMBL=ENSG00000116062
TAIR=locus=2095097
ENSEMBL=ENSG00000095002
MGI=MGI=101816
TAIR=locus=2131829
MGI=MGI=109519
ENSEMBL=ENSG00000113318

F

Seeded From PANTHER


PTHR11361:AN26

GO:0005634: nucleus

ISS: Inferred from Sequence or Structural Similarity: TAIR=locus=2092404
SGD:S000002313
MGI=MGI=1329021
GeneDB_Spombe:SPCC285.16c
SGD:S000002504
MGI=MGI=1343961
SGD:S000005450
GeneDB_Spombe:SPBC19G7.01c
MGI=MGI=101816
RGD:620786
TAIR=locus=2130913
SGD=S000001891
MGI=MGI=1860077
SGD:S000000688
GeneDB_Spombe:SPAC8F11.03

C

Seeded From PANTHER


PTHR11361:AN26

GO:0007126: meiosis

ISS: Inferred from Sequence or Structural Similarity: TAIR=locus=2092404
SGD:S000002313
MGI=MGI=1329021
SGD:S000002504
FB=FBgn0036486
TAIR=locus=2095097
SGD:S000005450
TAIR=locus=2130913
SGD=S000001891
MGI=MGI=1860077
SGD=S000001162
SGD:S000000688
GeneDB_Spombe:SPAC8F11.03

P

Seeded From PANTHER


PTHR11361:AN161

GO:0003006: reproductive developmental process

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=101816
SGD=S000005450
GeneDB_Spombe=SPBC19G7.01c

P

Seeded From PANTHER


PTHR11361:AN161

GO:0005524: ATP binding

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000095002
SGD:S000005450

F

Seeded From PANTHER


PTHR11361:AN161

GO:0005634: nucleus

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=101816
RGD:620786
SGD:S000005450
GeneDB_Spombe:SPBC19G7.01c
ENSEMBL=ENSG00000095002

C

Seeded From PANTHER


PTHR11361:AN161

GO:0016887: ATPase activity

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000095002
MGI=MGI=101816
SGD:S000005450

F

Seeded From PANTHER


PTHR11361:AN161

GO:0032300: mismatch repair complex

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000095002
MGI=MGI=101816
SGD:S000005450

C

Seeded From PANTHER


PTHR11361:AN161

GO:0043570: maintenance of DNA repeat elements

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000095002
ZFIN:ZDB-GENE-040426-2932
FB:FBgn0015546
GeneDB_Spombe:SPBC19G7.01c

P

Seeded From PANTHER


PTHR11361:AN79

GO:0003684: damaged DNA binding

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=1343961
TAIR=locus=2132233
ENSEMBL=ENSG00000116062

F

Seeded From PANTHER


PTHR11361:AN159

GO:0003684: damaged DNA binding

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=101816
TAIR=locus=2095097

F

Seeded From PANTHER


PTHR11361:AN159

GO:0006298: mismatch repair

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000095002
MGI=MGI=101816
FB:FBgn0015546
SGD:S000005450
GeneDB_Spombe:SPBC19G7.01c
TAIR=locus=2095097

P

Seeded From PANTHER


PTHR11361:AN159

GO:0030983: mismatched DNA binding

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=101816
TAIR=locus=2095097

F

Seeded From PANTHER


PTHR11361:AN81

GO:0005524: ATP binding

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000116062
SGD:S000002504

F

Seeded From PANTHER


PTHR11361:AN81

GO:0005634: nucleus

ISS: Inferred from Sequence or Structural Similarity: SGD:S000002504
GeneDB_Spombe:SPCC285.16c
ENSEMBL=ENSG00000116062
MGI=MGI=1343961

C

Seeded From PANTHER


PTHR11361:AN81

GO:0006298: mismatch repair

ISS: Inferred from Sequence or Structural Similarity: MGI=MGI=1343961
SGD=S000002504
GeneDB_Spombe=SPCC285.16c
FB=FBgn0036486

P

Seeded From PANTHER


PTHR11361:AN81

GO:0016887: ATPase activity

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000116062
SGD:S000002504

F

Seeded From PANTHER


PTHR11361:AN81

GO:0030983: mismatched DNA binding

ISS: Inferred from Sequence or Structural Similarity: ZFIN:ZDB-GENE-020905-3
ENSEMBL=ENSG00000116062
MGI=MGI=1343961
SGD=S000002504

F

Seeded From PANTHER


PTHR11361:AN81

GO:0043570: maintenance of DNA repeat elements

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000116062
ZFIN:ZDB-GENE-020905-3
GeneDB_Spombe:SPCC285.16c

P

Seeded From PANTHER


PTHR11361:AN292

GO:0005634: nucleus

ISS: Inferred from Sequence or Structural Similarity: SGD:S000000688
GeneDB_Spombe:SPAC8F11.03
ENSEMBL=ENSG00000113318

C

Seeded From PANTHER


PTHR11361:AN292

GO:0006298: mismatch repair

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000113318
MGI=MGI=109519
SGD:S000000688

P

Seeded From PANTHER


PTHR11361:AN292

GO:0006310: DNA recombination

ISS: Inferred from Sequence or Structural Similarity: SGD:S000000688
GeneDB_Spombe=SPAC8F11.03
ENSEMBL=ENSG00000113318

P

Seeded From PANTHER


PTHR11361:AN292

GO:0043570: maintenance of DNA repeat elements

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000113318
GeneDB_Spombe:SPAC8F11.03

P

Seeded From PANTHER


PTHR11361:AN170

GO:0006301: postreplication repair

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000095002
MGI=MGI=101816

P

Seeded From PANTHER


PTHR11361:AN279

GO:0007126: meiosis

ISS: Inferred from Sequence or Structural Similarity: SGD:S000000688
ENSEMBL=ENSG00000113318
MGI=MGI=109519
GeneDB_Spombe=SPAC8F11.03

P

Seeded From PANTHER


PTHR11361:AN278

GO:0030983: mismatched DNA binding

ISS: Inferred from Sequence or Structural Similarity: ENSEMBL:ENSG00000113318
SGD=S000000688
SGD=S000001162
TAIR=locus=2131829

F

Seeded From PANTHER


PTHR11361:AN228

GO:0032502: developmental process

ISS: Inferred from Sequence or Structural Similarity: WB:WBGene00001872
MGI=MGI=1860077

P

Seeded From PANTHER



See also

References

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