Physical Entity: Create core set of fields for a derived physical entity, catalogued object from a "specimen". ie DNA extract etc

[rintoult]

GIVEN I have accessed DINA as collection manager

WHEN I access a physical entity

THEN I expect to have access to a core set of fields that are specific to the object under view

AND be able to search on them.

[rintoult]

I expect there will be many linkages derived from the process used to generate these physical entitites. I also assume that some of this design work has already occurred in the "Sequence Database" portion of DINA which exists in the test instance.

For CCFC there are two main categories of Physical Entities= Catalogued Objects that need homes and data. I will describe them in two separate comments so the conversations can easily be split up. They are Specimen Replicates and Samples in SeqDB parlance.

[rintoult]

Specimen Replicates: the multi copies of each accession preserved and stored in our collection, these have a life span so at some point are destroyed, have parent to child relationships between themselves. Here are the current fields associated: Specimen Replicate Name Version Specimen Replicate Parent Name Specimen Replicate Parent Version Start Date (yyyy-mm-dd) Revival Date (yyyy-mm-dd) Date Destroyed (yyyy-mm-dd) State - method of preservation, how material is preserved Cryo, freeze dried, living slant etc Storage Medium - the growth media associated Contents - we use this to track the cryoprotectants or culture overlays Amount or Size of Sample Collected - not used Notes Preparation Protocol Group - limits the protocols to be associated Preparation Protocol Name - this would be the preparation process in the new schema Collection Code Group - this field is linked to the specimen record, might be different collection in some cases, but not often for collection purposes Collection Code this field is linked to the specimen record, might be different collection in some cases, but not often for collection purposes Specimen Identifier this field is linked to the specimen record, might be different collection in some cases, but not often for collection purposes Sub ID this field is linked to the specimen record, might be different collection in some cases, but not often for collection purposes Container Name - would be associated from the "storage module" Well Row - would be associated from the "storage module" Well Column - would be associated from the "storage module"

[rintoult]

Samples in SeqDB are anything derived from a Specimen Replicate, in our case the Specimen Records are only data the Specimen Replicates are what have a physical presence and from which other entities can be derived. The fields listed below are completely biased towards DNA since it is the most used type of Sample. Also for collection purposes DNA extracts would probably be the main thing we would have in our archive?

-- sample properties -- |  

-- | -- sample.name = Sample Name | ID number or name which relates to specimen sample.experimenter = Experimenter | Person who carried out the sample prep i.e. DNA extraction sample.version = Version | Suffix added to distinguish samples derived from the same specimen (eg. A,B,C) sample.versionDescription = Version Description | Describes specific sample preparation process or source for each sample version (Eg. Second extraction or second DNA elution from same process) sample.source = Source | Type of specimen or portion of specimen used for sample, ie herbarium material, fresh spores, front leg of insect sample.kit = Kit | Technique or commercial kit used to produce sample. sample.dnaNotes = DNA Notes | Description of sample; ie quality or total quantity of DNA sample.dnaConcentration= DNA ng/\u00b5L | Numeric value of sample concentration, DNA or RNA sample.date= Extraction Date(yyyy-mm-dd) | Date extraction carried out. sample.notes=Notes | Field for further description of the sample

[rintoult]

We currently host the following types of samples in SeqDB - not sure how many we want to also capture in DINA.

Sample Type: Chemical, DNA, WGS, Library, Protein, RNA

I realised that there are more fields than are listed in the glossary I have been stealing from here are those fields.

Sample Group Name

Sample Name Version Sample Type: Either Chemical, DNA, Library, Protein, RNA Experimenter Extraction Batch Extraction Date (yyyy-mm-dd) Version Description Source Growth Media Sample Concentration (ng/μL) Sample Concentration Notes Kit Group Name Product/Kit Name Tube ID Nucleic Acid Extraction DNA Concentration per starting material Unusable sample (True/False) Date Discarded (yyyy-mm-dd) Discarded Notes Initial sample pellet size (mL) Lysis buffer volume (mL) Proteinase K volume (mL) Ratio 260/280 (protein) Ratio 260/230 (polysac.) Quantification method DNA Notes Sample Notes Inoculation Date Fraction Fermentation Temperature Fermentation Time Extraction Solvent Protocol Group Name Protocol Name Collection Code Group Collection Code Specimen Source Type: Write S for Specimen or MS for Mixed Specimen Specimen or Mixed Specimen Identifier Sub ID Specimen Replicate Version (If source type S) Container Group Name Container Name Well Row Well Column Date Archived (YYYY-MM) Sample Storage Location Sample Storage Conditions Amount Available Pre-Treatment Alternative Contact Information Project Tags Last Modified

[banchinic]

For our collection, we need samples or something similar to host our DNA extracts and the preserved spores in vials that we sell. I don't want to create Physical Entities for each vial because I sometimes have hundreds of the same strain and that makes it very difficult to follow when mixed with our actual pot cultures in the greenhouse. All pertinent fields for samples for our collection have been identified by Tara's comments (We don't use all those fields).