Schema: Miscellaneous Tables

Machine-Scored Data

Machine-Scored data is data assigned to images automatically by a scanning machine, such as the Chromavision ACIS.  A MachineSession is the machine-scoring of 1 scan.  We may want to have multiple MachineSessions per scan.  One MachineSession might be for a brown color, while another machine session might be for a blue color.  Or perhaps one MachineSession might be for only circled area in images, and another MachineSession the entire image.  

In addition, data from our custom image analysis program (JCorn) also appear in the MachineScores table.

Schema of the Machine-Scored Data related tables


Schema of Sessions-related tables

Papers Table: Represents papers that a pathologist has written in which sessions from TMAJ are referenced.  The table PapersSessions associates papers with the sessions they reference.
PaperSessions Table: A many to many table that links papers to sessions.  Each paper is simply a collection of published sessions that a user wants other people to see (associated with a paper).
RecentSessions Table: A many-To-many table associated users with sessions along with a timestamp.  This allows a list to be displayed to the user showing their most recently accessed sessions.
ScoringStrategy Table: Every session may be assigned a scoring strategy.  A scoring strategy is a collection of dynamic fieldnames in the ScoredImageFields table.  So the dynamic fields that are given for an image depend on 2 things: the tissue-type the user selects, and the scoring strategy of the session. 
Sessions Table: A user scoring an individual scan.  (A user may wish to score a scan multiple times; for example, maybe they want to come back 3 months later and re-score the images to see if the results agree.)  The table scans represents the scanning of an ArraySlide.
SessionsUsers Table: A many-To-many table allowing users to share their session with other users.  Users have access to their own sessions (indicated by the UserID column in the Sessions table), plus any sessions in this table that match their UserID.

Tissue-Related Tables

TMAJ has several tables used for tracking tissue.  The use of these tables is optional, and not directly related to tissue micro-arrays. 

AnimalExperiments Table: The AnimalExperiments table is linked to the Specimens Table.  Some blocks are taken from animal experiments.  
BlockOrSlideExchanges Table: A simple table used to keep track of where tissue has been sent.
BlockUsagesAlt Table: Represents any kind of usage of a block.  Slides may go into this table.  Or if block tissue is ground-up and used this table may also be used.
CellLineExperiments Table: Some tissue diagnoses (sub-blocks) actually come from cell-lines.
Slides Tables: These are regular slides (as opposed to array-slides.)  These slides contain tissue from only 1 block.

The schema for Tissue-Related Tables (Specimens, Blocks, Sub-Blocks) in TMAJ.

Miscellaneous Tables

DataUpdates Table: A table used to log changes that users make.
DataDeletes Table: Similar to DataUpdates, but this table logs deletions that users make.
Enumerations Table: A table used as a master "Lookup Table".  Contains lists of choices for various groupNames(GroupName is a column in the Enumerations Table.)
Grants Table:  Represents a grant.  This table is external and not related to any tables in TMAJ.
KeyValues Table: A table that acts as lines would in a config file.  For example, if in a config file you say a key-value pair (like username = tmaj1), the KeyName would be username and the KeyValue would be tmaj1.
Protocols Table: Represents permission obtained from a hospital's IRB (Internal Review Board) to carry out a scientific experiment.  This table is not related to any other tables in TMAJ.  At this point, it is only used to record information. 

Schema of miscellaneous tables in TMAJ

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