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ORCAE Help wiki

Getting started

The website is best viewed with Firefox but can be viewed with any browser (although the layout might differ slightly with other browsers). If you want to use the full functionality of the portal (to view protein alignments and to work on gene structure using Artemis and/or GenomeView) you will need to have Java Web Start installed.

Access to the annotation section is restricted to the annotators so you will need to register and log in before you're able to annotate the genome. Registered users have full access to all sections of the portal. Once you have logged in, you start a new session and you don't have to fill in your login information again as long as your session is active. Note that when you are idle (not doing anything while being logged in) for too long your session will expire and for security reasons you will be logged out automatically, if you want to continue working you will have to login again.

To be invited to create an account you should send a request by email to the project coordinator or to the general email address beg-orcae@psb.ugent.be

After logging in you will be redirected to the home page of your account. There you will find an overview of all the genomes you have access to. For each genome you will be presented with a list of links to the different subsections of the annotation portal (eg. Annotation, Search, Workbench, etc). Also, a list will be provided of your 5 most recent modifications to that genome.

When you edit a locus a new record will be created in the database. The previous records are not deleted, however, so the database retains all previous annotations. You can always look back at previous versions of a locus using the history. To view an older version, select the date of modification from the dropdown menu. Note, however, that when you modify a record it is always the latest version that is modified (even if you were looking at an older version).

As soon as you modified a locus you become the “owner” of that locus and your name will be shown in the annotator field. As soon as the default owner name (Eugene) is no longer present the monitoring system will be active for that locus. This means that the owner of a locus will automatically be notified by mail if someone has changed that particular locus.

Functionally Annotating a Gene

There are no mandatory fields to be filled in. This means that you can enter annotations in just one field or in all the annotatable fields and this information will be entered into the database.

To add an annotation to a locus click on the “Modify This Record” button. When you click the “Modify this Record” button (also available in the side-bar menu) a pop-up window will be opened. This way you can make modifications while still having all the info available from the view page. In the edit section most of the fields of the view page are editable. To submit your changes click on the “Submit Your Changes” button on the Edit page. After submitting your modifications, they will be validated and the edit page will close automatically after 10 sec (or click 'continue'). On closure of the edit page the view page will reload to show the newly entered information. If you modified the structure of a gene model, that locus will be temporarily locked (status: in update). During this time the similarity information (blast, InterPro, ESTs, …) will be updated, when this is finished the locus will again become available for edit (the context view is updated immediately and will reflect the new situation).

Duration of an update is 15-20min depending on server load and protein length.

The gene page is divided into several sections (Annotator, Gene Function, etc). Each section is described in detail below. Note that a comment field is available in each section of the gene page. Here you can enter general comments relevant to that section of the gene page. Use this field to provide additional information about the genes and to note things like conflicts in the annotations provided, errors you are unable to correct, etc. When the conflict is with an annotation entered by another manual annotator, or when you have a question/remark regarding previous manual annotations, you are encouraged to communicate directly with the previous annotator (his/her contact information can be found in the Annotator block).

The Artemini / GenomeView applet

The gene structure can be altered by using the online Artemis tool (Artemini) or GenomeView in the edit-section. Artemis is a gene visualisation and editing application developed by the Sanger institute. You can obtain some help with using this application from http://www.sanger.ac.uk/Software/Artemis/v7/manual/. GenomeView is a new genome annotation tool developed by our own group. Opposite to Artemini it can visualise many more types of data. More info can be found at http://genomeview.sourceforge.net/ .

More information on how to use GenomeView and detailed descriptions on the interface can be found here

Use the Artemis window to edit the gene structure and save your modifications to enter them into the database. Note that the window only shows part of the supercontig but the coordinates are the same as on the supercontig. When you start an Artemis session the locus will be temporarily unavailable for other annotators to edit. Be sure, when you have finished working in Artemis, to close the Artemis window so that the locus will again be available for other annotators.

It's possible to enter “new” genes (or to split existing ones). To do so just make a new CDS in artemini and it will be entered in the DB as a new locus. You don't have to enter a locusID for the new gene, this will be done automatically (the new ID will be the last ID on the contig +1). When you split a gene, the one spanning the largest genomic region will inherit the locusID while the shorter one(s) receive new ID(s). You can even create new genes in introns of other genes. Also different sorts of RNA genes can be entered (tRNA, rRNA, miRNA, …), refer to the list provide in the artemini edit view to check which kind of RNA are accepted. (Also RNA genes will receive a locusID as described for the protein coding genes).

To help you in the annotation you now have the possibility to create many more 'features' eg. intron, repeat, … , see the dropdown list in the top left corner of the edit screen for the full list of possibilities. Keep in mind that only the CDS and RNA features will end up in the database, all others will be ignored! Also less common type of proteins can be entered in ORCAE through the artemini/GenomeView as for example SelenoCysteine proteins. To do so create a “normal” gene but add the qualifier /type=“SeCys” in the gene edit window of artemini or GenomeView. This way some of the basic checks done on submitted gene structures will be skipped (eg. The in-frame stop-check in case of SeCys proteins). Also pseudo genes can be submitted this way. Therefore add the qualifier /pseudo or /type=“pseudo” in the gene edit window (almost all checks will be skipped). Proteins submitted this way will be tagged accordingly (normal genes have tag 'mRNA', Secys have 'Secys', …).

If you modify gene structures, then loci that overlap with your gene will become obsolete (=permanently locked for edit) and will accordingly be flagged in the DB. Overlap is determined by sequence comparison. If a neighbouring gene has more than 50 bases (with 98% similarity) in common with your gene that whole locus will be considered as obsolete, this also happens if your gene does not cover all the exons of that gene. If you encounter such a case and want to keep the not covered exons in the database, you split of the not covered exons and with the leftover exons you create a new gene (CDS). Genes that have become obsolete will no longer be included in the previous/next navigation nor in the context overview. They are however not deleted but you can only go to their view page by surfing directly to them (eg. by searching for that locus).

 
help/help.txt · Last modified: 2013/02/05 15:55 by listeAdmin
 
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