Revision as of 20:20, 28 January 2010

This is the discussion page for the Chado Natural Diversity Module Working Group. Notes on what we talk about and what decisions are made will be posted here. Eventually, as we settle on specific outcomes, those outcomes will be posted to the main page, and eventually reflected in the Chado schema.

At this time (January 2010), most of this discussion is about making changes relative to the version that was created in 2007 with Heliconius in mind. This is referred to below as HDB.

We will also use what came up at the PAG meeting as starting point for the discussion. This will change over time, as things settle down.

Responsibilities

Note: These responsibilities are flexible. They are just what we decided at the PAG meetings. They are wide open to discussion (or just add your name below.

Sook Jung will take the lead on schema changes/development. Sook is interested and is motivated to produce a working schema as soon as possible.

Dave Clements will lead documentation efforts. Dave will produce wiki documentation for the new tables. I hope to also create schema diagrams (probably using Power Architect). Dave is also keenly interested in how phenotypes are represented both in this module, and in the rest of the Chado.

Add your name here ...

January 2010

Observational Taxonomy

HDB has several different levels of biological unit, all represented with a different set of tables

• Organism - This already exists and comes from the Chado Organism Module. It defines a species.
• Biotype
• Stock (which is different from the stock table already in Chado)
• Individual
• Crossexperiment
• Specimen

And there are a bevy of relationships between these tables.

All of this tables describe some unit/group of biology/life, ranging from species (organism) down to tissue in hand (specimen). The HDB design has several structurally identical tables in HDB for the various levels for different types of data (phenotype, images, ...). This particular hierarchy is also particular to butterflies.

Stock

Both the HDB version and the production Chado have a stock table. The Chado Stock Module was added to production Chado while or after the HDB version was being developed.

The Chado Stock module is about keeping track of lines in your lab/community. Someone needs to take a look at it and determine how the natural diversity module should interact with it.

Observational Taxonomy Proposal

When Sook Jung mapped the HDB version to tree biology a number of issues came up, many of which boil down to:

• Species/biotype/stock/individual/cross hierarchy doesn't work for trees (living trees, not abstract ones).
• Lineage doesn't work for trees.

This highlights that HDB is not a very Chadoesque design. We need to genericize the design to support arbitrary hierarchies, lineages, and mating types. This will support many more users and allow them to store images, phenotypes, genotypes, properties, etc. for whatever level of the hierarchy they have data for.

We can't touch Organism, as it's a key table in every Chado instance out there. However, everything else is open to change.

Observational Unit

Specifics:

1. Try to combine biotype, stock, individual, and crossexperiemt into a single table, tentatively called obs_unit (with a nod to GDPDM).
2. Investigate also folding specimen into obs_unit.
3. An observational unit's place in the observational taxonomy will be indicated by a new column in obs_unit that points to the CV table. For butterflies, the possible values might be "species", "biotype", "stock", "individual", and possibly "specimen"

Observational Unit Relationships

We need to support arbitrary M:M relationships between different levels of the observational taxonomy, and within the same level as well. For example, we may want a complete chain from species to individual (or plot or brood or ...), and that individual may have resulted from crossing 2 other individuals (or from cloning one, or ...).

The common solution is to create a bridge/mapping/intersection table to implement M:M relationships between obs_unit and itself. This table would define the standard "subject relationship object" triple where the subject and object are obs_unit's and the relationship is a CV term.

This also deals with complications in lineage and mating types. You can represent T. Thermophila which has 7 mating types (any 2 will do), C. elegans which has hermaphrodites and outcrossing, E. coli which is asexual, ...

It was pointed out that this table may contain cycles. In some experiments an individual will be crossed with it's descendents. Therefore software that walks these relationships will need to detect cycles.

Current Status

We're planning on moving ahead with merging the existing tables into a single table. And, no we can't yet agree on that table name.

Project/Experiment/Study Hierarchy

The current Project table is defined in the General Module. The HDB design links to it extensively. However, other modules hardly use it at all.

The GDR group needs to the ability to more robustly define projects/studies, and to introduce substudies/project hierarchy, as well.

Phenotypes and Genotypes

Phenotypes

Phenotypes are not particularly well defined in Chado. Scott says that there are two sets of phenotype tables in Chado. One is a first rough draft that snuck in (and is used by some), and the other is a more robust set, which is used by others (including FlyBase). Too make things worse, which tables are in which set is not presently clearly defined.

Dave C. will do some research into

1. What is currently going on in Chado?
   • Which tables are in the old and new implementations?
   • How are those tables currently used, and by whom?
2. What are best practices for representing phenotypes in a generic database like Chado?

If items #2 and #1 don't line up, and there are not a lot of current users, then I would like to look into

1. reimplementing phenotypes in Chado, and
2. providing migration paths for what users we do have.

HDB Design

The HDB version of the module ties into the preexisting phenotype table.

Genotypes

Genotypes appear to be more clearly defined in the production Chado schema: A genotype is a collection of features.

Assays, Images

HDB includes support for images and assays. We should probably have a general purpose solution that is usable for all images and assays, not just those in the natural diversity module.

February 2010

The first meeting in February will be held Monday February 8, at 11am Eastern US. Between now and then we'll run a Doodle poll to determine the best time to have regularly scheduled meetings. This will be tough as we have key interested parties in Europe and across the contiguous US.