Guidelines for the Community Annotation of the CYORF Database

Shown below are the guidelines for the annotators of CYORF. The guidelines, which include some technical recommendations, are set to facilitate the community annotation of the cyanobacterial genomes. Please follow them as far as possible. Send your questions and opinions to the system administrator or to any of the coordinators.

1. General 2. Annotating CYORF

1. General

1-1. Scope and objectives

The aim of this project is to help the cyanobacteriological community develop a database containing reliable information about the function of each gene on the completely sequenced genomes: Synechocystis sp. strain PCC 6803, Anabaena sp. strain PCC 7120, and many more. A task of this magnitude is beyond the reach of any small group of people and must draw on the expertise of the community as a whole, whose knowledge forms the basis of the CYORF database. Information in most databases is presented without justification, making it difficult for the user to assess the degree of confidence it warrants. We hope to avoid this problem by having each assertion tied to a reference, a citation to a research paper or to unpublished results (see Section 1-4). The database will be most useful to our community if annotations are entered with the user in mind. Please consider how users might find the gene you are annotating in a "keyword search" for a set of functionally or structurally related genes. To that end, before editing the "Description" field of a gene, please examine the style and wording of the descriptions of related genes.

1-2. On-line annotation

With your username and password, you can access the annotators' version of CYORF. You can add new annotations to, or revise annotations of, any ORF on-line. The results will be immediately incorporated in the public version of CYORF with your username shown in the "Last annotator" field. As you annotate, please consider how a naive user might try to find the gene through a keyword search. To refine your annotation, you may revise it over and again. You can overwrite your annotation within 24 h without the record of correction or refinement in the HISTORY of the gene; a query box will ask you whether you are overwriting your previous annotation or whether you are creating a new version. You can view the previous versions of annotation by using the HISTORY command.

1-3. Community annotation

Any annotator is free to annotate any gene within the database, although many of the annotators are likely to annotate their favorite areas. When you revise annotations of a certain gene, the annotator of the previous version will be automatically notified of the revision. It may be useful to contact previous annotators beforehand. You might also be asked by the previous "last annotator" for discussion after the revision. It is to be expected that different annotators may sometimes have different views about the characteristics of a gene product. In such cases, constructive discussions, such as those that routinely take place during scientific meetings, can be very helpful. It isn't necessary for annotators to agree on all particulars. In such cases, the alternative views may both appear in the annotation. However, if you feel uncomfortable about even that arrangement, then please contact the system administrator, who may be called upon to make the final decision.

If you find typographic errors and minor mistakes, please notify the last annotator. Minor errors and mistakes may also be corrected by the coordinators. Upon correction by the coordinators, the word "edited" is added to the "Last annotator" field. The last annotator will be automatically notified of the correction.

1-4. The basis for annotation

Any new information added to a database should be accompanied by support, in the form of citation of a published paper, a submitted manuscript, or unpublished observations. You can cite a published paper by entering its PubMed ID (see Section 2-6.). If the paper relevant to your annotation is in press or submitted, define a "local reference" and cite it in the "Reference" field (see Section 2-6.). You can also make annotations on the basis of your unpublished results by defining a local reference (see Section 2-6.).

1-5. Linkage with CyanoBase

Updates in CYORF are weekly sent to the Kazusa DNA Research Institute and used for updating CyanoBase. It is to be noted, however, that CYORF and CyanoBase are distinct entities, and ultimately, Kazusa DNA Research Institute decides for itself what annotations are to appear in CyanoBase. The annotations within the databases therefore may not always be the same.

2. Annotating CYORF

2-1. How to open the "Edit" window

Select the gene to be annotated by using the "Search ORFs" function. In the "Search Result" window, click the "ORF ID" (e.g., sll0045, alr1213. etc.) of the gene to open the window for editing. You can edit four fields, i.e., "Gene name", "Description", "Memo", and "Comment", and incorporate appropriate references to the "Reference" field. When you need to edit other fields, please contact the system administrator.

2-2. The "Gene name" field

Currently, about 1,400 ORFs in the Synechocystis genome have a gene name(s). For the sake of identification of the gene by gene name search, alternative gene names and obsolete gene names are also shown in the "Gene name" field.

To give a new name to a gene, you need to cite a reference showing the experimental or logical basis for the name. The reference can be a published paper(s), an in press or submitted paper of yours, or your unpublished results. If you propose a gene identity based on similarity to another gene for which there is experimental justification, please cite the literature for the reference gene and show the degree of similarity in the "Comment" field. For citation of the materials having no PubMed ID, you need to define a "local reference" (see Section 2-6). Add the new name to the left of other gene names when the "Gene name" field already contains some name(s). Please do not remove the existing name(s) unless you believe it essential to do so. When you delete a gene name, explain the reason in the "Comment" field (see sll1082 and its "History" for example).

2-3. The "Description" field

Give short phrases showing the nature of the gene product and its biochemical and physiological functions, e.g., "periplasmic protein, function unknown", "xxxase, involved in ...", "cAMP receptor protein, essential for motility", "zzz-like protein, function unknown.". Use the "Comment" field for description of other information (see below).

2-4. The "Memo" field

This is for annotators' memorandums and not visible in the public version of CYORF.

2-5. The "Comment" field

Give whatever information that may help understanding of the structure and function of the gene. These will include transcriptional regulation, possible alternative to the proposed initiation codon, mutant phenotype (not necessarily in Synechocystis sp. strain PCC 6803 and Anabaena sp. strain PCC 7120), post-translational modification, etc. Since CYORF refers to "CyanoMutants" at Kazusa DNA Research Institute, please deposit the characteristics of the mutants in CyanoMutants and refrain from detailing the mutant phenotype in the "Comment" field.

2-6. The "Reference" field

Cite the papers that describe determination of the biochemical function and/or physiological roles of the gene product. If the function of the gene (and hence the gene name) was first determined in other organisms, including other strains of cyanobacteria, cite the papers in those organisms. Even in the latter case, remember to cite the papers that deal with the gene of Synechocystis sp. strain PCC 6803 and Anabaena sp. strain PCC 7120, if there is any.

To cite a paper in the "Reference" field, enter its PubMed ID into the "PubMed ID" box and press the "Get reference" button. Use the "PubMed search" box to find the relevant paper and its PubMed ID. To cite a paper without PubMed ID (e.g., some old papers, book articles, etc.), press the "local reference" button and define a "local reference ID" for the paper. You can enter the local reference ID into the "PubMed ID" box to cite the paper in the "Reference" field. We recommend to use "(family name + initials) of the first author + year of publication + a, b, c..." as the local reference ID (e.g., SuzukiI1993a).

You can define your in press or submitted paper as a local reference and cite it in the Reference field. You can also refer to your unpublished results by defining a local reference (see also Section 1-4). To define a local reference, open the "local reference" window and follow the instruction there.

2-7. Confirmation of the update

After sending your annotations to CYORF, re-load the data to see your new annotation in the "Search Result" window. Use the "History" button in the editing window to make sure that each of your annotations has been properly incorporated in each appropriate data field. Each annotation in CYORF is associated with a version number, currently 1.0, which will be incremented with each change, e.g. to 1.1, 1.2, and so on. For the genes having only "Version 1" annotation in their HISTORY, the gene description is unchanged from that initially prepared by the annotators at Bioinformatics Center, Kyoto University. The genes whose annotation has been checked by a cyanobacteriologist have a "Version 0.1" annotation as well, which shows the initial description of the gene.

The use of the version field is somewhat different in Anabaena than in Synechocystis. Currently, 99% of the ORFs in Anabaena have the "Version 1" annotations, which means that no cyanobacteriologist has touched them since the launching of the Anabaena genome. By revising the annotation, the version will be updated from 1 to 2. If you think that the initial annotation is good enough, press the "Submit" button in the "Edit" window, even if you have not made any changes. This will not change the annotation but will update the version from 1 to 2, indicating that a human has checked the annotation. (This function is not available in the Synechocystis genome).

Last updated: October 15, 2002
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