Guidelines for literature-based curation: Difference between revisions
(Created page with '==Literature based/Manual GO annotations== Annotation is the process of assigning GO terms to gene products. Annotations can be made either from published literature or manually…') |
No edit summary |
||
| Line 2: | Line 2: | ||
Annotation is the process of assigning GO terms to gene products. Annotations can be made either from published literature or manually by comparing sequences or can be inferred using automated methods. Literature based annotations are from published papers and inferring annotations from them is very time-consuming but produces very high quality, species-specific annotation, and brings the information about the gene product into a format in which it can be used in high-throughput experiments. This is an extremely worthwhile process in the long term. It may be best carried out by people who know the function of the gene product, and the associated biology, in great detail; for example experimental scientists who are familiar with the published literature. If you are doing this, then you may like to write and suggest modifications to the ontology structure as well. | Annotation is the process of assigning GO terms to gene products. Annotations can be made either from published literature or manually by comparing sequences or can be inferred using automated methods. Literature based annotations are from published papers and inferring annotations from them is very time-consuming but produces very high quality, species-specific annotation, and brings the information about the gene product into a format in which it can be used in high-throughput experiments. This is an extremely worthwhile process in the long term. It may be best carried out by people who know the function of the gene product, and the associated biology, in great detail; for example experimental scientists who are familiar with the published literature. If you are doing this, then you may like to write and suggest modifications to the ontology structure as well. | ||
==Steps involved in Literature Based curation== | |||
[Flow chart] | |||
==Key aspects of literature based annotations== | ==Key aspects of literature based annotations== | ||
The most difficult task in doing literature based annotations is in figuring out the correct GO term and the evidence code to use in the annotation. The GOC has identified some areas of the ontology that are more tricky to figure out than others and has come up with guidelines to help curators map the data/results presented in the paper to the right GO term. They are listed below. | |||
The most difficult task in doing literature based annotations is in figuring out the correct GO term and the evidence code to use in the annotation. The GOC has come up with | |||
==Guidelines for Annotating to Downstream Processes== | ==Guidelines for Annotating to Downstream Processes== | ||
| Line 14: | Line 16: | ||
==Guidelines for annotating using 'regulation of xx' terms== | ==Guidelines for annotating using 'regulation of xx' terms== | ||
==Manual Sequence based annotations== | |||
(Use last section of text from Emily's Electronic annotation section) | |||
(Use flow chart from JCVI, currently available on the GOC) | |||
Revision as of 14:12, 31 August 2010
Literature based/Manual GO annotations
Annotation is the process of assigning GO terms to gene products. Annotations can be made either from published literature or manually by comparing sequences or can be inferred using automated methods. Literature based annotations are from published papers and inferring annotations from them is very time-consuming but produces very high quality, species-specific annotation, and brings the information about the gene product into a format in which it can be used in high-throughput experiments. This is an extremely worthwhile process in the long term. It may be best carried out by people who know the function of the gene product, and the associated biology, in great detail; for example experimental scientists who are familiar with the published literature. If you are doing this, then you may like to write and suggest modifications to the ontology structure as well.
Steps involved in Literature Based curation
[Flow chart]
Key aspects of literature based annotations
The most difficult task in doing literature based annotations is in figuring out the correct GO term and the evidence code to use in the annotation. The GOC has identified some areas of the ontology that are more tricky to figure out than others and has come up with guidelines to help curators map the data/results presented in the paper to the right GO term. They are listed below.
Guidelines for Annotating to Downstream Processes
Guidelines for annotating using 'Binding' terms
Guidelines for annotating using 'response to xx' terms
Guidelines for annotating using 'regulation of xx' terms
Manual Sequence based annotations
(Use last section of text from Emily's Electronic annotation section) (Use flow chart from JCVI, currently available on the GOC)