Add some plan/objective specification terms

[obi-bot]

Some plan/objective specification terms are required to be added to OBI by MGED ontology (MO) group. These are experimental design types in MGED ontology and generally used in MAGE-TAB files by transcriptome community. Details see the attached file. I listed the MO terms, IDs, definitions, and the suggested superclassed in OBI.

Reported by: zhengj2007

Original Ticket: obi/obi-terms/430

[obi-bot]

AddTermsReqest

Original comment by: zhengj2007

[obi-bot]

Group the Design Type terms in 6 categories

Original comment by: zhengj2007

[obi-bot]

Chris and I discussed the terms we submitted and categorized them in 5 different patterns. Some terms we need to check their usages before decide which patterns they are belong to.

The details were in the attached file: DesignType-20100215.xls

Original comment by: zhengj2007

[obi-bot]

• priority: 5 --> 7
• assigned_to: jamesmalone --> jzheng24

Original comment by: zhengj2007

[obi-bot]

In MO, we have some terms to describe what an investigation studies and the techniques are used in the experiment, which could be added as subclass of OBI: study design.

For a study design, it has part some objective specification. With objective specification, it could link the study design to assay and the assays shared the same objective can be retrieved easily. For example, we can have 'transcript identification design' has part 'transcript identification objective' which is achieved by 'transcription profiling'. 'transcript identification objective' can be achieved by other assays, eg. RT-PCR.

In this case, I think it is useful to have more specific molecular feature identification objective such as 'transcript identification objective'. For example, I am going to study transcript. For pulling all the assays with 'transcript identification objective', I can find out which kind of assays and related protocols I can use for my investigations.

For some study designs, they can be examined by almost all kind of assays and techniques. For example, 'disease state design' which pathological condition of a part, organ, or system of an organism is studied. There are two options to add an objective specification with the disease_state_design, 1. add a specific objective specification such as disease identification objective as a subclass of organism feature
2. using restriction: has part some objective specification is about some disease

In this case, I don't think it is very useful to have 'disease identification objective'. The option 2 notices people that disease should be indicated somewhere in the investigation and can be used for validation of experiment annotations. For example, in a MAGE-TAB file, characteristics of disease should be provided.

Need comments and suggestions on it.

Original comment by: zhengj2007

[obi-bot]

• priority: 7 --> 8

Original comment by: zhengj2007

[obi-bot]

An experimental design (MO) (which is 'study design' in OBI) will specify the overall design of an experiment which include 1. objective specification specify the objective of the experiment, such as protein and DNA interaction identification objective 2. independent variable specification specify what the experimental factor varied in the experiment 3. what technology used in the experiment, such as microarray, high throughput sequencing

Please see the attached figure that have a generic template and 5 examples.

An OWL file has been created (ExpDesign.owl) of the request terms with logical and textual definition for review.

ExpDesign.owl checked in the same directory of obi.owl

Original comment by: zhengj2007

[obi-bot]

Design template

Original comment by: zhengj2007

[obi-bot]

Submitted terms were discussed on San Diego OBI workshop on Mar 22, 2011 and were approved to be added into OBI.

Chris and Jie will work on it

Original comment by: zhengj2007

[obi-bot]

DONE. Terms were added in.

Original comment by: zhengj2007

[obi-bot]

• status: open --> closed

Original comment by: zhengj2007