obi-bot
commented
14 years ago Design pattern
A X is a specimen that is the output of some storage process with an objective of material maintenance Need to create corresponding storage process and specify inputs and outputs
frozen_sample ------------- frozen specimen and freezing process have been added following the pattern. Suggest modify the label to freezing storage.
agar stab --------- An agar stab is a specimen that is output of an agar stab storage process An agar stab storage process is a storage process with input cell culture and agar and output agar stab.
paraffin_sample --------------- A paraffin specimen is a specimen that is output of a paraffin storage process. A paraffin storage process is a storage process with input organism or anatomical entity and paraffin and output paraffin specimen with an objective of material maintenance.
freeze_dried_sample ------------------- A freeze dried specimen is a specimen that is output of a lyophilized storage process which specimen is lyophilized for storage. A lyophilized storage process is a storage process with input material entity and output freeze dried specimen with an objective of material maintenance.
Actually, frozen, agar stab, paraffin embedded, lyophilization is a way to prepare the specimen for long term storage. So far, I think we do not need to distinguish storage preparation and real storage process to avoid over-modeling.
fresh_sample ------------ 'specimen' define by a specimen creation process with specimen creation objective which is to obtain and store a material entity for potential use as an input during an investigation Specimen creation process included both obtain and store processes. Can we modify specimen creation process which is to obtain or to obtain and store?
Fresh specimen is a specimen that is output of a specimen creation process without storage. Stored specimen is a specimen that is output of a specimen creation process with storage.
Or define fresh specimen using disjoint (Chris' suggestion) A fresh specimen is a specimen and is disjoint from stored specimen [ frozen specimen and agar stab and paraffin specimen and ..]
Any other suggestion?
Original comment by: zhengj2007
Some MO terms were used in MAGE-TAB files to describe how the specimens which used for an microarray experiment were maintained.
Those terms were listed as fellow: agar_stab agar stab, a cell culture inoculated into agar for long term storage freeze_dried_sample A biomaterial that has been lyophilized or dried by freezing under a vacuum. fresh_sample A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat. frozen_sample A biomaterial obtained frozen paraffin_sample A biomaterial obtained embedded in paraffin (wax).
All these material entities are the specified output of a storage process.
Suggest add to be subclasses of OBI_0100051 specimen with restriction: is specified output of some 'storage'
Labels and Definitions of terms will be modified if needed.
Reported by: zhengj2007
Original Ticket: obi/obi-terms/519