**Specimen Life Cycle Use Cases**\
Penn: no comments

TJU no comments

**1. Actor: collection protocol designer**\
A CP designer wants to add an (arbitrary) event to the list of events,
with its own details (a sort of "dynamic extension" for events, not just
for static elements). The designer wants to add an event with its own
attributes and be able to share its meaning with other sites. Entry
forms should be created.

Indiana: Useful feature

*Pitt: Need to think about how the added attributes might interact with
temporal queries.*

**2. Actors: tissue bank tech, research coordinator**\
A tissue bank tech and a research coordinator want to communicate about
specimen-related events occurring for the protocol, with the system
facilitating the communication and storing data about it.

*Pitt: Communicate how? Automated emailing from the system? A message
page that both can look at? This needs much more thought.*

**3. Actors: collection protocol designer**\
A CP designer wants to specify a series of collection points that repeat
indefinitely. The collection points within the series occur at specified
intervals. If one event is delayed, the subsequent events are postponed
by the same (or different?) amount of time.

Indiana: The study calendar functionality provides a way to specify a
series of collection points. Offsets (delays) in collection can be
tracked and a subsequent shift in the anticipated collection dates is
applied on all future collection groups

Yale: This is important for our clinical trials at Yale Cancer Center.

*Pitt: not as important for us in the near future -- we don't do a lot
of prospective collection.*

**4. Actors: banker, investigator, system**\
A banker wants to supply thaw time to the investigator when it is
distributed; be able to print the "biosketch" and provide it to the
investigator, or allow the investigator to look it up.

**5. Actor: technician, PI**\
Dr. Smith (the PI) requests certain pre-acquisition variables to be
captured in caTissue.

Indiana: collection protocol needs to ask for required events; useful
feature

Yale: This needs to be expanded. Is this something that can be collected
in a dynamic extension on patient, or just recording events that happen
before actual collection?

*Pitt: please be careful about adding anything required or complicating
any further the definition or display of a collection protocol.*

**6. Actor: banker**\
A banker has a predefined name for the specimen collection group,
provided with the biospecimens (and thus not under the bank's control).
It is available to the bank at the time the specimens are received, not
before. (e.g. not at the time the CP is defined) Actor must be able to
assign this name as the name of the SCG. The labeling convention for
specimens is based on that pre-defined name.

*Pitt: This is our use case for labels. Not sure it goes into Specimen
Lifecycle. Does not currently need to be defined per CP; maybe per
repository.*

Indiana is supporting this format of label generation for the specimens.
The label generator is configurable and the specimen label format is
{SCGname}/'some constant string'. Such a format can be defined for each
specimen (collected, derived, aliquoted.)

*Pitt: regarding bug 7405: OK not to have uniqueness constraint on
labels.*

Bug 7405: Unique constraint on labels could pose a problem for the
multi-site use case

CaTissue has a unique constraint on the storage container, specimen
labels etc.

With the Multi-site use case under discussion this could pose a problem
as many sites might use the same naming convention, and would have to
intentionally change their labeling design.

To avoid this specimen labels need to be more specific, for eg: the
specimen labels should be unique within a collection protocol as well as
across collection protocols

To avoid this problem with the legacy data migration from multiple sites
into a single instance, unique constraints on the labels should be
removed

**7. Actor: bank administrator**\
The banker imports data into caTissue from an existing system and there
is a need to use the SCG and specimen names from the legacy data in the
SCG and specimen name fields of caTissue.

Indiana: Bug 7405 (detailed above) should be considered for this use
case

**Indiana: Label generator**

**[Use]{.underline}**

CaTissue provides support for label generator plug in. The
SpecimenCollectionGroup name and Specimen label format could be
specified here.

Drawback of this approach is that labels can be custom generated but
label format remains same across the entire application. Which means it
is not possible to have different format for different
SpecimenCollectionGroup or Specimen (based on the collection protocol).

**[Solution]{.underline}**

Solution to this problem is that label format be specified for every
collection protocol event and specimen requirement while generating the
collection protocol definition. This format will then eventually be used
as a template and label are accordingly assigned at the label generation
time.

Label format would consist of variables and constant string. Variables
are replaced by actual values at the runtime. Anything in curly
braces'{}' indicate a variable.

For example for SCG label format can be -- {PPI}/wk1.

Where PPI is Participant Protocol Identifier, which would be replaced at
runtime. So if PPI is OS01 then generated label would be -- OS01/wk1.

Similarly Specimen can have label format like {SCGN}-P etc.

There are a few predefined variables which can be used in specifying
format. These variables are -- SCGN, PPI, ID, PSL, PROT, SITE, PCN

**[Current situation and workaround]{.underline}**

This label format needs to be stored somewhere. However in caTissue
Suite v1.0 there is no convenient position to store and retrieve this
format for the SpecimenCollectionGroup.

For Specimens however, the label attribute in the Specimen object can be
used to store the labelFormat

For specimens in caTissue Suite v1.0, the label formats are stored.

While inserting the actual specimens, there is no direct way (link) to
insert specimens corresponding to the original specimen requirement.

For SpecimenCollectionRequirementGroup there is no attribute where the
nameFormat can be stored.

Bug has been logged for direct link from Specimen to Specimen definition
(bug# 7072), and moving name attribute to
AbstractSpecimenCollectionGroup (bug# 7073).

To circumvent this problem, we use a workaround where we store SCG
nameFormat in a separate table. The nameFormat would be pulled in from
this table and and the SCG name would be generated.

For Specimens the real problem is that currently there is no link to
Specimen definition from Specimen object. But this could be retrieved by
keeping specimens in specimen requirement unique.(at certain level they
should have different quantity, class, type so that specimen could be
matched with corresponding specimen definition)

**8. Actor: banker, system**\
Tracking container temperature -Not currently in caTISSUE - events on
storage containers for temperature monitoring (This could be part of the
bio-sketch)

*Pitt: not high priority. Is the idea here to actually create an
interface with the freezer and monitor this electronically, or to have a
tech enter the information every N hours, or ??*

**9. Actor: banker**\
When setting up the protocol the banker also sets up the anticipated
processing events. (So they are captured at set up, and can just click
to say it occurred in CP Based View) -and account for exceptions when
the anticipated events do not end up occurring

This is an important feature to minimize data entry time for the end
users

This bug is still present in Suite RC3 where all aliquots get the same
quantity if the protocol is defined from the application UI. A manual
edition would be required to change the quantity of each aliquot in the
collection protocol definition.

While defining the specimen requirements in the collection protocol, we
define all the specimens that are to be collected as well as all the
child specimens that are to be created. We can specify the quantity of
parent specimens and derived specimens, but not for aliquots. Many
protocols store aliquots in different quantities to avoid freeze thaw
cycles and to maximize space and ease of shipping specimens out fast.
Since the quantity cannot be specified for each aliquot the quantity has
to be added for each aliquot in a separate step by clicking on each
individual aliquot separately. We have logged an enhancement for the
same in bugzilla bug \# 5759 which requests for the aliquots to be
displayed in the summary page while saving the collection protocol.

Yale: This is important for us for our Pathology Tissue Services group.

**10. Actor: technician**\
When processing a specimen (tissue processing & slide processing), there
is a defined SOP. If this SOP is not followed exactly, the tech must
record the exact deviation.

Yale: This needs to be something that is enabled on a per-protocol
basis. Not all protocols may be interested in following this, even if
they probably should

*Pitt: agree with Yale*

**11. Actor: system, PI**\
Capability to upload files (e.g. PDF) with scientific results & attach
these to specimens & aliquots (Not just providing a link, but actually
storing the file in the db)

Indiana: 80% of our data are large files eg Gb per sample and could not
be stored in caTissue. Almost all of the high throughput data is too
complex to be stored in caTissue; all our data is therefore stored off
line. It also has implication for IRB since storing it in two locations
allows to minimize the risk for subjects.

YaleAlso, provide the capability to see easily-displayed formats
(images, text) within the application without linking out to the raw
file URL

*Pitt: would be nice to be able to upload consent documents, IRB
protocols, but it would be up to the user to have the appropriate
application for viewing the attachment (pdf, Word, whatever). If we get
into images, should we consider integration with a separate application
rather than trying to do this in caTissue?*

**Additional comments from Indiana**

Indiana: Typical workflow for Specimen handling for serum and plasma
that will automatically create some of the data points required for the
life cycles of specimens

All use cases start with the workflow required from printing out labels
and forms used for the consenting and sample (e.g. blood tubes) and data
collection in the clinic. In a second step most specimens such as blood
are spun and split into aliquots, which again requires the printing of
labels. All specimens should be easily track-able from the time they
leave the patient until they are consumed in a research experiment.

**At the Collection Site:**

-   To do that, the research assistant (RA) takes a consent form, a data
    collection form, and a sheet with a set of pre-printed barcode
    labels from a pile (these pre-printed labels are the result of
    another workflow that is not directly related to the specimen
    collection workflow, assuming that enough label sheets are always
    available).

-   The RA peels one label off and sticks it on the data collection
    form. The RA peels another label from the label sheet and is sticks
    it on the consent form.

-   If the patient has a regular patient-label in the clinic, the RA
    will stick that label on the first page of the data collection form.

-   The RA fills the data collection form with basic data elements on
    the participant and collection, some of which are dynamic
    extensions.

-   The RA takes specimen collection tubes from the stock of unlabeled
    tubes at the clinic, and labels them by peeling off the respective
    labels from the label sheet and sticking them on the tubes.

-   The RA identifies the appropriate labels on the label sheet either
    by recognizing the specific label format and markings, or by
    instruction (hints) printed on the label sheet next to the label
    stickers.

-   Finally the RA clips data collection form, consent, and the label
    sheet together in this order, and places them on a tray with the
    empty labeled tubes on top.

-   Authorized RA, nurse, or physician collects specimen into those
    tubes and places the filled tubes back onto the tray. The RA or a
    transport runner picks up the tray and brings it to the biobank.

**At the Biobank:**

-   The technician scans the primary specimen tubes which will create
    the Received event in the caTissue system for these specimens.

-   Then the technician walks to the centrifuge and scans the centrifuge
    followed by the vials as she places them into the centrifuge. Next
    the technician sets the timer of the centrifuge to 10 min (as
    proscribed by the standard operating procedures, SOP) and scans the
    on-button of the centrifuge as she turns it on. This establishes the
    spin-down event time point for caTissue.

-   Now the technician places the scanner device back into the cradle,
    which will invoke a process to save the data and send it into the
    caTissue application.

-   The technician looks over the forms, especially checks the consent
    for completeness. Then the technician goes to the caTissue
    application and selects a general search text-box and using another
    barcode scanner attached to the computer terminal she scans the
    collection form barcode. (The collection form is the hardcopy
    representation of the Specimen Collection Group and the barcode is
    the SCG barcode.)

-   The technician then transcribes the data from the collection form.
    This includes editing the detail on the Participant, the
    Registration, Consent form and tiers, then back to the SCG and any
    dynamic extensions. The existence of the collected specimens is
    already visible in the application from the earlier scan of the
    tubes.

-   By the time the technician is done transcribing the data, the 10 min
    since the start of the centrifuge are over and the centrifuge run is
    completed.

-   The technician now continues the process of deriving plasma,
    platelet poor plasma, cells, etc. as required by the standard
    operating procedures (SOP) for the protocol.

-   Eventually all derived specimens must be filled into aliquot vials.
    For this protocol, 18 vials are used, 9 for serum, 5 for plasma, 4
    for platelet poor plasma.

-   The technician takes 18 unlabeled vials and [sticks labels from the
    label sheet]{.mark} onto these vials and puts the vials into a
    holder and pipettes out the aliquots.

-   Technician will accept the collection group in caTissue suite and
    aliquots will be placed in the allocated storage spaces in the
    freezer.