What kind of genomic data should be in the CADB?

As I see it now, a basic unit of information in CADB is a CA amino acid sequence (that belong to certain organism, family, subgroup, etc.) and for most CAs this info can be taken from Uniprot. To be specific, let's consider all CAs of mouse from UniProt and particularly CA with accn. Q64444. The question is what genomic information (chromosome num., exons, introns, transcripts, etc.) for Q64444 has to be in the CADB? Which source is better to use for getting genomic-related data? Ensembl?
Then, regarding what we discussed on meeting last time: coordinates. In case of Q64444 (and assuming we agree on taking coordinates from Ensembl) we have the following 'Ensembl' coordinates: Chromosome 11, 84,771,290-84,779,546. As I understood Csaba, these coordinates may be changed in next Ensembl releases. In fact, such changes are ok but this means that we need to have some routine that would be run once in a while to check/update coordinates (as well as, likely, something else). So, what kind of solution on coordinates may we have?

Installation Issues

The wiki for the CADB has been created, and I have been informed by the admin that Catalyst as well as Template Toolkit has been installed. DS should try and test to ensure that all the necessary plugins are there. The admin promised to install any missing plugin as soon as he is informed, so I think we should verify that we have an installation complete enough for the purpose of this project. On my part, I will carry out my Catalyst tutorial sessions on the system, so as to ensure, in my limited capacity, that all the features specified in the material I am using work correctly. Additionally, I have confirmed that modperl is on the system.

Databases with similar functionality

Could you please have a look at the "Databases of individual protein families" mentioned in NAR Database List? I wonder functionality of which databases resemble the one of CaDB as we have in mind?

Wiki

Was reading up some things on the wiki stuff, and from what I read, the wiki needs an sql database to work, as well as apache. I think these should be on the server in our group somewhere, but I am quite sure I dont have the permission to work on that right now. Kindly enlighten me if I am wrong about this. But if I am right, then I will need to be given a user right on the right machine so that I can connect through ssh and do what needs to be done, and also whoever is in charge would need to create a new user on the MySql database, assign necessary privileges and give me the username and password. If these are not possible, he could as well install the wiki and give me editing rights so that I can go on with managing the system.

Is this blog secure from external viewers?

Well, here I am! I had an account before, so the naming of my blog account may not conform to the one specified by Dennis. My name will appear as Phemmy. But I do hope this is okay. One side of this blog that I may like to discuss is the security of the information we have on here. Is it hidden from other online users. Just thought I should ask, in case some other people interested in something like this stumble on it and decide to do something funny.

-AO

Technical info

This post is about software to use.

• Web server: Apache (http://www.apache.org), it is likely that we also need the mod_perl installed
  
• Database server: MySQL (http://www.mysql.com)
  
• Web framework: Catalyst (http://www.catalystframework.org)
• 
  

I chose the Catalyst since it is in Perl and we all have a certain level of expertise in Perl. If there are better suggestions for a web framework let's discuss them. With the Catalyst, web pages are typically generated with the help of Template-Toolkit Perl library (http://template-toolkit.org).

Wiki-related stuff

This week I checked several wiki-systems (list of wiki-systems). My initial thoughts were that perhaps one of these systems may provide us with wiki-functionality for editing entities stored in a database. If it was the case we wouldn't need to think how to store the versioning information (i.e., history of modifications) in our database. After reviewing a couple of systems I realized that wiki-systems are predominantly for editing regular web pages. That is, they operate on the level of a document or a page (a document may consist of some text plus a couple of 'database' entities) rather than on the level of 'database' entities themselves.

In this way, I suggest to use the following 'wiki-architecture':

• Database that doesn't store history/modification/etc. information (well, some info about history has to be stored anyway but, at least, database will store only current versions of objects, e.g., CA sequences)
• Wiki for documentation related to the database (will have such editable pages as 'About database', 'Schedule', 'How to work with database', 'Database schema', 'People involved', 'Related publications', 'Design&implementation information', etc.) and for CA sequences (as I see this now, for each CA sequence we generate a corresponding wiki-page that can be editable by everyone or by certain people only, the wiki-system will be responsible for storing history of changes, and from time to time approved changes will be added to the database)
  

Ayodeji, would you mind if you would be responsible for the wiki for our database? You then need to install a wiki-system on one of the IMT machines. MediaWiki might be a good choice I think. Of course, we can use the already working wiki if such exists on the IMT machines. Right after installation you can create several documentation pages (i.e., 'About database', , 'Schedule', etc.). Wiki-pages with data from CA-database will be generated later when we'll create an initial db-design and populate the db with example data.