experimental manipulations

[stevevanhooser]

Hi all -

Is there any part of NIF that deals with experimental manipulations?

For example, common experimental manipulations in developing animals are monocular deprivation by lid suture, enucleation (removal of an eye), deafening, etc. These might have a value associated with them, such as date of onset or offset.

As an example, one might want to express the following:

right eye lid suture onset at postnatal day 12
right eye lid suture offset at postnatal day 21
left eye lid suture onset at postnatal day 21
right eye lid suture onset at postnatal day 26

(these aren't the best experiment, but just an example of some events that one might want to specify for an experimental animal)

We have a ton of these we'd like to express for our lab.

The closest I found are these clinical read codes but I don't think this is what we want:
https://bioportal.bioontology.org/ontologies/RCD?p=classes&conceptid=72170

Thanks
Steve

[tgbugs]

These would be covered as part of the methods ontology. http://ontology.neuinfo.org/trees/query/subClassOf/ilxtr:technique
For example, there is blinding technique http://uri.interlex.org/tgbugs/uris/indexes/ontologies/methods/177 (resolves to http://uri.interlex.org/base/ilx_0739724), but we don't have some of the other ones. If you have a full list of these we can add them.

You can capture this information generically use the techniques.

subject was-participant-in-performance-of protocol-performance-1
protocol-performance-1 employs-technique blinding
protocol-performance-1 start-date (some date)
protocol-performance-1 start-time (some time)

[stevevanhooser]

Thanks Tom

I have a couple more questions.

Here is a list of putative techniques:

Sensory deprivation technique	Description
Dark-rearing	The raising and housing of animals in a completely light-free environment
Eyelid suture	The closing of an eye by surgical suture
Eyelid suture removal	The removal of eyelid sutures, allowing natural eye opening
Retinal silencing	Removal of neural activity of the retina without damage to retinal cellular structures
Retinal enucleation	Surgical removal of the eye

Question 1: some of these techniques can be applied to either the right or left eye. Would we develop a separate "technique" for each eye, or apply it to, say, UBERON:0004548 ("left eye") somehow? How would that be coded?

Question 2: Is there a list of the attributes of protocols, that includes the words "was-participant-in-performance-of", "employs-technique", "start-date", "start-time", etc?

Thanks
Steve