Swiss-Prot keywords SPKW2GO: Difference between revisions
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Swiss-Prot entries are assigned keywords manually based on literature and sequence analysis checks by curators. In addition, TrEMBL entries are assigned keywords automatically from two sources; | ==Method== | ||
Swiss-Prot entries are assigned keywords manually based on literature and sequence analysis checks by curators. | |||
In addition, TrEMBL entries are assigned keywords automatically from two sources; | |||
*initially, as the TrEMBL entry is first created, based on keywords in the nucleotide sequence entry | *initially, as the TrEMBL entry is first created, based on keywords in the nucleotide sequence entry | ||
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*subsequently, during automatic annotation, by two programs | *subsequently, during automatic annotation, by two programs | ||
a. RuleBase – which uses manually curated rules | |||
b. Spearmint – which is an automatic system based on decision trees | |||
Keywords are mapped to corresponding GO terms in the SPKW2GO file, which was originally constructed manually by MGI curators and is now maintained by the UniProtKB-GOA team at EBI. The mappings are then transitively assigned at each UniProtKB-GOA release. GO annotations using this technique will receive the evidence code Inferred from Electronic Annotation (IEA). | Keywords are mapped to corresponding GO terms in the SPKW2GO file, which was originally constructed manually by MGI curators and is now maintained by the UniProtKB-GOA team at EBI. The mappings are then transitively assigned at each UniProtKB-GOA release. GO annotations using this technique will receive the evidence code Inferred from Electronic Annotation (IEA). | ||
This method has been evaluated at 91-98% accurate (Camon et. al., 2005). | This method has been evaluated at 91-98% accurate (Camon et. al., 2005). | ||
==Mapping file== | |||
The SPKW2GO mapping file is available at: | The SPKW2GO mapping file is available at: | ||
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==Example== | |||
The Swiss-Prot keyword ‘Cell junction’ (KW-0965) has been assigned to the Angiomotin protein (UniProtKB accession Q4VCS5). A mapping was manually created between this keyword and the GO term ‘cell junction’ (GO:0030054). Therefore, Angiomotin, and any other protein associated with KW-0965, will automatically be assigned the GO term ‘cell junction’. | |||
The annotations created by SPKW2GO mapping are displayed in the UniProtKB-GOA gene association files (Fig. 1), the keyword will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate that this method has the GO reference: GO_REF:0000004. SPKW2GO annotations can also be viewed in QuickGO. | The annotations created by SPKW2GO mapping are displayed in the UniProtKB-GOA gene association files (Fig. 1), the keyword will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate that this method has the GO reference: GO_REF:0000004. SPKW2GO annotations can also be viewed in QuickGO. | ||
==References== | |||
Camon et. al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 6 Suppl. 1:S17 | Camon et. al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 6 Suppl. 1:S17 | ||
Revision as of 06:28, 21 June 2010
Method
Swiss-Prot entries are assigned keywords manually based on literature and sequence analysis checks by curators. In addition, TrEMBL entries are assigned keywords automatically from two sources;
- initially, as the TrEMBL entry is first created, based on keywords in the nucleotide sequence entry
- subsequently, during automatic annotation, by two programs
a. RuleBase – which uses manually curated rules b. Spearmint – which is an automatic system based on decision trees
Keywords are mapped to corresponding GO terms in the SPKW2GO file, which was originally constructed manually by MGI curators and is now maintained by the UniProtKB-GOA team at EBI. The mappings are then transitively assigned at each UniProtKB-GOA release. GO annotations using this technique will receive the evidence code Inferred from Electronic Annotation (IEA).
This method has been evaluated at 91-98% accurate (Camon et. al., 2005).
Mapping file
The SPKW2GO mapping file is available at: http://www.geneontology.org/external2go/spkw2go.
Example
The Swiss-Prot keyword ‘Cell junction’ (KW-0965) has been assigned to the Angiomotin protein (UniProtKB accession Q4VCS5). A mapping was manually created between this keyword and the GO term ‘cell junction’ (GO:0030054). Therefore, Angiomotin, and any other protein associated with KW-0965, will automatically be assigned the GO term ‘cell junction’.
The annotations created by SPKW2GO mapping are displayed in the UniProtKB-GOA gene association files (Fig. 1), the keyword will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate that this method has the GO reference: GO_REF:0000004. SPKW2GO annotations can also be viewed in QuickGO.
References
Camon et. al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 6 Suppl. 1:S17