Database Tables

About this Document

Primary Keys are underlined. SpecimenID
Required fields are in bold: SurgPathNumber
The fields that uniquely identify the record (primary key excluded) have a * attached. Example: SurgPathNumber*, HospitalID*
--Knowing the SurgPathNumber and the HospitalID uniquely identifies one row of the Specimens table.
Columns are either type-in, enumerated, a date, true/false, or numeric
If the column name is enumerated, the Example Value will appear in brackets. Example {Johns Hopkins}

ArrayBlocks

A block with tissue from two or more "normal" blocks. This "special" block is in the format of any array, where each coordinate may be from a different block.

ArrayBlocks Table
Column Name	Type	Description	Example Value
ArrayBlockID	num	the primary key	65
ArrayName *	text	the name of this arrayblock; generally a short description of why it was created.	Human Prostate Array
Source	text	the person for whom the array is being created	De Marzo
NumberOfRows	num	the number of rows in this ArrayBlock.	20
NumberOfColumns	num	the number of columns in this ArrayBlock.	20
IsFinal	bool	true if the ArrayBlock can not be modified in the ArrayBuilder application anymore.	No
Creator	text	The technician who created the ArrayBlock	C. Southerland
Purpose	text	The reason the ArrayBlock was created	Staining normal human tissue
CreateDate	date	The date construction began on the ArrayBlock	07-01-2008
FinalDate	date	The date the ArrayBlock was completed	07-02-2008
Status	text	The current status on construction of this arrayblock	cancelled
NumberOfSpots	num	How many spots/images are on the Arrayblock; Generally 400	400
CoreSize	float	The size of each of the ArrayCores on this ArrayBlock. (in millimeters). Usually 0.6, 1.0, or 1.5	0.6

ArrayCores

An ArrayCore is a "cylinder" that is placed into an ArrayBlock at a defined x and y position on the ArrayBlock. This "cylinder" is actually a piece of tissue from a regular block (not an arrayBlock). The tissueDiagnosisID tells us which regular block this piece of tissue belongs to before it was placed in an ArrayBlocks. This table in a sense in a link between the tissue in regular blocks and the tissue in ArrayBlocks.

ArrayCores Table
Column Name	Type	Description	Example Value
ArrayCoreID	num	the primary key	7877
ArrayBlockID *	num	the ID of the ArrayBlock in which this core has been placed	2
X *	num	The x location of this cylinder (x starts at 1 and moves from left to right across the array)	1
Y *	num	The y location of this cylinder (y starts at 1 and moves from top to bottom across the array)	20
TissueDiagnosisID	num	The tissueDiagnosisID, which tells us the regular block from where this tissue was obtained	54
Control	text	This field may be used instead of a tissueDiagnosisID to tell us from where the tissue originated. Sometimes a researcher just wants to put in control tissue, and not specify the details of the tissue. If this is done, the tissueDiagnosisID field gets a default value, and a brief description of the control tissue (such as "bladder") is entered into this column	bladder
OutsideArrayCoreID	text	If an outside research institution uses its own system for labelling ArrayCores, this column may be used. Note: This column currently is not used in TMAJ	h-404

ArrayImages

A jpeg image of one coordinate on an arraySlide. These are also called spots. In a 20 x 20 arraySlide, there would be 400 spots.

ArrayImages Table
Column Name	Type	Description	Example Value
ArrayImageID	num	the primary key	543312
ArrayCoreID*	num	the ArrayCore (cylinder) of this ArrayImage. (contains X & Y position.)	3431
ScanID *	num	the Scan of this ArrayImage (links to ArraySlide, which contains Z position.)	811
DirectoryPath	text	the directory under the main images directory where this image is stored. All ArrayImages with the same scanID have the same value for the DirectoryPath, although this is not a requirement.	TMA_0017_CUT_020_SCAN_01_HE_0_BLISS
Filename	text	the filename of the image.	0_0_12_14_0_0_42321.jpg
IsBad	bool	true if the image is blurred or mostly blank space, and a waste of time for the user to even view. (Bad images are skipped over the Images-Manager program to save time.)	No
WebSlideURL	text	the URL a user may see additional information on the image provided by the BLISS machine. (not an actively used feature)

ArraySlides

A "cut" from an ArrayBlock. The first cut is z = 1, the second is z = 2, and so on. A slide is 2 dimensional and can be put under a microscope and viewed, whereas a 3 dimension block could not be.

ArraySlides Table
Column Name	Type	Description	Example Value
ArraySlideID	num	The primary key	1015
ArrayBlockID *	num	The ArrayBlock from which this ArraySlide was cut.	17
Z *	num	The cut number of this ArraySlide. The first cut is 1, the second is 2, and so-on.	25
Stain	text	Either the antibody name this ArraySlide was been stained with (example: KI67), or H-and-E. The ArraySlide is always stained prior to scanning, otherwise the tissue would be clear.	H&E
StainingUserID	enum	The technician who stained this ArraySlide	{John Smith}
ContactUserID	enum	The person to contact to obtain this ArraySlide	{John Smith}
ExperimentNumber	text	The experiment number this ArraySlide is in.	JH9999
Location	text	Where this ArraySlide is currently located	DeMarzo Office

Blocks

Normal, (non-array) ordinary, blocks. These are obtained by taking tissue from a specimen and putting it into paraffin. Later, tissue from these "normal" blocks are extracted and put into an ArrayBlock.

Blocks Table
Column Name	Type	Description	Example Value
BlockID	num	The primary key	122
SpecimenID *	num	The specimen from which this block was cut. One specimen generally yields many blocks	715
BlockDesignation *	text	The letter written on the block.	A
Part *	text	The part number of the specimen from which this block came.	2
Fixation	enum	How the block was fixed	{Formalin}
Area_mm2	text	The surface area of the block	111.0
OutsideBlockNumber	text	The block identifier, if the block is from a different institution	T3432
ContactUserID	enum	The person to contact to obtain this block.	{John Smith}
Not_Infile_Location	text	The location of the block if it has been given to somebody else. (not in our lab)	XYZ Lab
HasHandE	bool	true if this block has an H&E slide	Yes
IsDivided	bool	true if this block has been cut into 2 or more parts	Yes
BlockStatusID	enum	Choice between Good,Intermediate, Poor, or Cut-Through. (The block is cut many times to make slides).	{Cut-Through}
CollectionDate	date	The date the block was taken from Surgical Pathology	05-01-2008

DataUpdates

A table whose sole purpose is for logging changes to data (except deletions). All the data in this table could be deleted, and the only information that would be lost is the logs. This table has been known to get quite large.

DataUpdates Table
Column Name	Type	Description	Example Value
ID	num	the primary key	343
TableNumber	num	Every database table is assigned a number that is hard-coded in the source code. See LogTable.java	3
PrimaryKeyID	num	the primary key of the record that was changed in the table. The tableNumber field and this field uniquely identify one record in TMAJ.	655
FieldName	text	The name of the column that was changed. The tableNumber, primaryKeyID, and this field uniquely identify one cell in TMAJ.	SurgPathNumber
UserID	num	The ID of the user who performed this change	4
NewValue	text	The new value the user assigned to the value	S93-98585
ChangeTime	date	The time the user made the change.	2008-04-01 15:30:00

Enumerations

Enumerations is essentially a "master lookup table". Lookup tables are defined as a table with 2 columns: an ID and a name. For example, Organs might be a lookup table where organID#1 is prostate, organID#2 is bladder, organID#3 is skin, etc. This table represents multiple lookup tables. The GroupName represents the collection. In our example, the GroupName would be called Organs. If we had 10 organs, there would be 10 rows each with the GroupName being the organ, and the ItemName being the name of the organ.

Enumerations Table
Column Name	Type	Description	Example Value
EnumID	num	the primary key	3
GroupName*	text	The group to which the item belongs. A group has one or more items in it. For example, a groupName called Organs might have items like: prostate, bladder, skin, etc. Examples of GroupNames in TMAJ: BlockFixations, BlockUsageDiagnoses, MarginsPositive, Organs, ProtocolCategory, ProtocolTypes, SpecimenFixations, AnimalTypes, BlockStatus, Diseases, MicroscopeUsers,	Organs
ItemName*	text	A choice in the group. If the groupName were Organs, a choice might be prostate.	Prostate

Hospitals

Represents hospitals from which a patient or specimen may originate. All patients and specimens are assigned a hospital.

Hospitals Table
Column Name	Type	Description	Example Value
HospitalID	num	the primary key	1
HospitalName*	text	The name of the hospital	Johns Hopkins

KeyValues

KeyValues is a way to store a "config file" in a database. Each line in the config file which has a key value pair is one record in this table. The advantage of keeping a config file in the database is that it will be backed up, and that it is easy to change. This table tends to be very small, as there are only a few config values placed in this table.

KeyValues Table
Column Name	Type	Description	Example Value
ID	num	the primary key	3
KeyName*	num	the name of the key, such as SPECIMEN_NUMBER, ARRAY_COLORS_TISSUE_TYPES, ARRAY_COLORS_ORGAN_TYPES, or MASTER_PASSWORD_HASH	MASTER_PASSWORD_HASH
KeyValue	num	The value of the key. For example for MASTER_PASSWORD_HASH, this would be the actual hash	/foa+gU3veyr4nGEn30ZnIv204Y=

MachineScores

A score for an ArrayImage that has been made by a machine such as the ACIS. For example, the machine may tell how much brown there was in the image. This table is only used if the user wants MachineScored analysis in addition to user-scored analysis.

MachineScores Table
Column Name	Type	Description	Example Value
MachineScoreID	num	the primary key	7623
MachineSessionID *	num	the MachineSessionID of the score. A MachineSessionID yields many MachineScores.	22
ArrayImageID *	num	the ArrayImage the MachineScored. An ArrayImage usually only has 1 MachineScore, but it may have more depending on how many MachineSessions are created.	12345
BrownArea	num	(An ACIS Field). The ACIS tells how much brown is in the image. Note: If it were the BLISS scoring, this is left null	205
BlueArea	num	(An ACIS Field). The ACIS tells how much blue is in the image. Note: If it were the BLISS scoring, this is left null.	14513
AverageBrownIntensity	num	(An ACIS Field). <check scanning machine docs for description> Note: If it were the BLISS scoring, this is left null.	240
Percentage	num	(An ACIS Field). The number of brown pixels related to the number of brown and blue pixels in a region. In other words, basically (brown pixels/brown + blue pixels). Note: If it were the BLISS scoring, this is left null.	5.99
Intensity	num	(An ACIS Field). The Average brown intensity of all pixels within a region scored. Note: If it were the BLISS scoring, this is left null.	220
Region Area	num	(An ACIS Field). <check scanning machine docs for description> Note: If it were the BLISS scoring, this is left null.	0
IHC_Area	num	(A BLISS Field). <check scanning machine docs for description> Note: If it were the ACIS scoring, this is left null	134.5
Avg_IHC_OD	num	(A BLISS Field). <check scanning machine docs for description> Note: If it were the ACIS scoring, this is left null	12.4
TotalArea	num	(A JCorn field) The total area of the image. Note: JCorn is an image analysis program made available by JHU.	1000000
MaskArea	num	(A JCorn field) The total area of the mask	50000
IntensityMinimum	num	(A JCorn field) The minimum intensity of the pixels in the mask	0
IntensityMaximum	num	(A JCorn field)The maximum intensity of the pixels in the mask	255

* not all fields are shown. Check the ACIS and BLISS documentation should you need the exact description of what the field represents. For programming purposes, their meanings are irrelevant other than the data type they store.

MachineSessions

A machine scoring all the images for a scan. A machine may score a scan several times, and get different scores each time for each spot. This is because the machine may be set at different thresholds.

MachineSessions Table
Column Name	Type	Description	Example Value
MachineSessionID	num	the primary key	62
ScanID *	num	The ArraySlide-Scan. When a scan is done, one or more MachineSessions may optionally be done with it.	12
ShortDescription*	num	a 20 character description that differentiates this MachineSession from other sessions assuming there is more than 1 session per scan. The majority of Scans however have at most one MachineSessionID.	threshold_50
MachineID	enum	The machine doing the scoring. This field may be unnecessary as it's also recorded in the Scans table, which is linked by ScanID.	{BLISS}
CreationDate	date	the date this machineScoring of a Scan was performed	2008-07-01
UserID	text	The user who initianed the MachineScoring	2
Notes	text	Any notes in addition to the ShortDescription the user wishes to record.	circled regions only

Papers

A collection of sessions in TMAJ (used for a published paper). Sometimes a user will publish a paper in a medical journal, and some of the data for that paper will be in TMAJ. The user then adds a new paper, and assigns all appropriate sessions to that paper (see PapersSessions table).

Papers Table
Column Name	Type	Description	Example Value
PaperID	num	the primary key	22
ShortTitle	text	a abbreviated form for the title	COX-2 Overexpression in PIA
Title	text	the full title of the paper	Cyclooxygenase-2 Is Up-Regulated in Proliferative Inflammatory Atrophy of the Prostate, but not in Prostate Carcinoma
UserID	text	the ID of the user who scored the images on TMAJ	{Angelo De Marzo}
PDFLink	text	a link to the paper	http://demarzolab.pathology.jhmi.edu/Reprints/Zha_Cox_2_Can_Res.pdf
PubMedLink	text	a link to the paper on pub med	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11751373
Abstract	blob	the full text of the abstract	...
Authors	text	all of the authors on the paper.	Shan Zha, Wesley R. Gage, Jurga Sauvageot, Elizabeth A. Saria, Mathew J. Putzi, Charles M. Ewing, Dennis A. Faith, William G. Nelson, Angelo M. De Marzo, and William B. Isaacs
JNLPLink	text	the url that a person can click that will automatically take them to the sessions for the paper in TMAJ.	http://www.tmaj.com/tma/paper_starter_1.jnlp

Patients

Represents a patient. All specimens originate from a patient. The use of this table is optional. Virtually all information in this table is HIPPA protected, and thus this table is often left blank. (If this table is blank, all specimens simply are assigned a default number (like 1) for a patientID. We simply put one dummy record in the patients table, and assign that patientID to every specimen.)

Patients Table
Column Name	Type	Description	Example Value
PatientID	num	the primary key	433
PatientNumber*	num	the unique number the hospital (in the field below) assigned to the patient	04-038931
HospitalID*	text	the hospital that assigned the patient number	1
NameFirst	text	the first name of the patient	John
NameLast	text	the last name of the patient	Smith
BirthDate	date	the birth date of the patient	01-15-1910
Race	text	the race of the patient	W
Sex	text	the sex of the patient	M
OutsidePatientNumber	num	Sometimes patients have more than one history number. This is a location for the 2nd history number.	P495-9391
OutsideHospital	text	The hospital that assigned the second history number	2

PapersSessions

A Many-To-Many table that allows us to determine what sessions a paper contains. A paper contains only published sessions. Papers represent published papers (say in a medical journal). Published sessions may be assigned to a paper, so that when a user goes looking for information from a published paper, it is easy to find.

PapersSessions Table
Column Name	Type	Description	Example Value
ID	num	the primary key	7877
PaperID*	num	the PaperID of a paper	2
SessionID*	num	the sessionID of a published sessions	505

Projects

A project is a collection of arraySlides. ArraySlides are organized into projects for security purposes (and for organizational purposes).

Projects Table
Column Name	Type	Description	Example Value
ProjectID	num	the primary key	4
ProjectName *	text	the name of the project;	Diagnosis Consensus
ProjectDescription	text	a brief description of the project	used for various pathologists to classify atrophy lesions
Source	text	the person responsible for the project	De Marzo
IsLookupDisabled	bool	true if sessions created in the project should not be able to see the original diagnoses in TissueDiagnosis. This means that in the Images app the image-info button will be disabled; Also, when the user shows the Data Table for the session, original diagnoses will not be displayed. Use this option to prevent users being biased by the original diagnosis.	No
AreTissueTypesRestricted	bool	true if the sessions created in the project may only choose TissueTypes chosen in the original diagnosis. So lets say there are 30 tissue types. Of these probably only 5 were used when the original ArrayBlock was designed in ArrayBuilder. This will ensure that only those 5 tissueTypes are shown in the drop-down box in the ArrayImage Frame. This option may help new users by restricting the options they can pick.	No

ProjectsArraySlides

A Many-To-Many table that allows us to determine what ArraySlides a project contains.

ProjectsArraySlides Table
Column Name	Type	Description	Example Value
ID	num	the primary key	7877
ProjectID*	num	the ProjectID of a Project	2
ArraySlideID*	num	the ArraySlideID of an ArraySlide that is in the Project	505

Protocols

A form that is sent to the Internal Review Board (IRB) at a hospital asking for permission to do a scientific experiment that involves either humans or animals. This table isn't linked to any other table in TMAJ, and using it is optional. It is for record-keeping only.

Protocols Table
Column Name	Type	Description	Example Value
ProtocolID	num	the primary key	25
ProtocolName	text	a short description of the protocol title	Approval to review pathology slides
PrincipalInvestigator	text	the lead person conducting the experiment (PI)	De Marzo
IRB_ProtocolNumber	text	the protocolNumber the Internal Review Board (IRB) assigns	98-05-12-15e
IRB_Contact1	text	the first point of contact at the IRB	{Jane Smith}

RecentSessions

Represents a user opening a session at a particular time. We use this table so we can pull a convenient list for users showing them the last 5 sessions they have accessed.

RecentSessions Table
Column Name	Type	Description	Example Value
ID	num	the primary key	251
UserID *	text	the userID of the user opening the session	51
SessionID *	text	the sessionID of the session the user is opening	25
LastAccessDate	text	the time the user is opening the session	2008-05-15

Scans

Represents a machine scanning 1 arraySlide. An arraySlide may be scanned multiple times by a machine. For example, 2 scans may have different resolutions, or different options for reading colors. Sometimes the end-user will want to keep both scans, even though they are of the same array-slide.

Scans Table
Column Name	Type	Description	Example Value
ScanID	num	The primary key	515
ArraySlideID *	num	The ArraySlide that was scanned	1015
ScanNumber *	num	The time that the ArraySlide was scanned. The first time is 1, the second is 2, etc. Most only have 1.	1
ScanningMachineID	enum	The machine that did the scanning of the ArraySlide	{BLISS}
Notes	text	If an ArraySlide is scanned more than once, this column should describe why 2 scans were necessary.	high resolution

ScoredImages

Represents a user scoring an arrayImage.

ScoredImages Table
Column Name	Type	Description	Example Value
ScoredImageID	num	the primary key	76343
SessionID*	num	the session the user created to score images	25
ArrayImageID*	num	the ArrayImage the user is scoring	255723
TissueTypeID	num	the new TissueTypeID the user assigns. This controls which dynamic fields will come up.	2
Notes	text	Any notes the user puts in the notes field.	2 areas of cancer

Shapes

Represents a shape a user draws on an image.

Shapes Table
Column Name	Type	Description	Example Value
ShapeID	num	the primary key	48193
ScoredImageID	num	the scoredImage the user onto which the user is drawing this shape	76343
Type	char	the first letter of the type of shape the user is drawing : line, circle, oval, text, etc.	O
x	num	The start x coordinate. (applicable for lines, circles, text, squares, and others.)	0
y	num	The start y coordinate.(applicable for lines, circles, text, squares, and others.)	0
x2	num	The end x coordinate (applicable for a line)	100
y2	num	The end y coordinate (applicable for a line)	50
TextDisplay	text	Only applicable for the text shape. This is the text .	"Cancer Region"
Width	num	the width of the shape, if applicable. It would be applicable in a rectangle.	100
Height	num	the width of the shape, if applicable. It would be applicable in a rectangle.	200
PointsList	text	Only applicable for the free-text shape. A string represents many x and y coordinates.	421,119;395,204;371,242;

Sessions

Represents a user scoring an entire scan (of an ArraySlide.)

Sessions Table
Column Name	Type	Description	Example Value
SessionID	num	the primary key	25
UserID *	num	the user who is the owner of this session	2
ProjectID*	num	the project this session was created under	3
ScanID *	num	the scanID whose ArrayImages the user is scoring in this session	54
SessionNumber *	num	starting at 1, this is incremented every time a user creates a new session with the same ProjectID/ScanID	1
IsPublished	bool	Same as IsFinal, and also means every other user of TMAJ can see this session	No
IsFinal	bool	true if the scoredImages of this session can no longer be modified	No
ScoringStrategyID	num	If set, the user may score all ScoredImageFields with this set ScoringStrategyID, when this session is scored.	2
CreationDate	date	the date when this session was created	2009-01-30
Notes	text	any additional notes the user wants to record about this session	rescored feb10

Slides

Represents an ordinary (non-array), slide. Slides are 2-dimension (glass) and can be placed under a microscope. This is an optional table in TMAJ, and is not required in normal TMAJ workflow.. Not all fields are shown.

Slides Table
Column Name	Type	Description	Example Value
SlideID	num	the primary key	45645
BlockID*	num	the block from where the slide was cut	122
CutDate	date	the date the block was cut and this slide was made	2008-05-20
CutNumber	num	The first cut of the block is 1, the second is 2, and so on.	20
Stain	text	What the slide was stained with	h & e
Location	text	Where the slide is	room 505, c331

Specimens

Represents all the tissue that comes out of a patient during a surgery. For example, a prostate.

Specimens Table
Column Name	Type	Description	Example Value
SpecimenID	num	The primary key. Automatically assigned by database.	12511
SurgPathNumber *	text	A unique number a hospital assigns to a specimen.	S01-99515
HospitalID *	enum	The hospital that assigned the SurgPathNumber.	{Johns Hopkins}
SpecimenTypeID	enum	The type, which will control which organ-specific fields are displayed for this specimen	{Radical Prostatectomy}
PatientID	num	Refers to the Patients table. One patient may have one or more specimens. If the patients table is not used, this may be given a default value (like 1).	5424
Age	num	The age of the patient at the time the specimen was taken	75
AnimalExperimentID	num	Used when the specimen is from an animal. This gives the associated experiment.	2
OutsideSurgPathNumber	text	A specimen may come to the local hospital from another hospital	T4541
OutsideResearchNumber	text	A Research Number that an outside institution assigns	R91-995011
SpecimenList	num	A list of any other specimens that came out of the patient during surgery	S01-99516^S01-99517
AccessionDate	date	The date the specimen was received by Surgical Pathology	06-12-2008
DateSpecimenTaken	date	The date of surgery	06-12-2008
Pathologists	num	The pathologists who diagnosed the specimen	John Smith
Physicians	text	The physicians associated with this specimen	Jane Doe
Notes	text	Additional notes on the specimen that do not fit into the normal columns	Specimen transferred
TumorBankNumber	text	The bank number where the specimen is stored	0585
FixationID	enum	The chemical or process that was used to ensure that the specimen does not decay.	{Ethanol }
MarginsPositive	enum	Is there cancer present in the patient's body along where the specimen was cut out. (e.g. did the surgeon not get all the cancer out?)	{No}
GrossDescription	text	a long description of giving the details of the specimen
Diagnosis	text	a long description giving the diagnosis of the specimen

SpecimenTypes

Represents the different types a specimen record may be. The type chosen will determine which dynamic fields are selected.

SpecimenTypes Table
Column Name	Type	Description	Example Value
SpecimenTypeID	num	the primary key	2
SpecimenTypeName*	text	the name of SpecimenType. Sometimes this is simply an Organ. Example: Kidney. Other institutions divide SpecimenTypes up by the surgery that was used to extract the organ. Example: Radical Prostatetomy.	Radical Prostatetomy

TissueDiagnosis

Also called a sub-block, this represents a circle on a block and includes a diagnosis of that area. This is the most specific area in the hiearchy that goes from patient to specimen to blocks to tissue-diagnosis.

TissueDiagnosis Table
Column Name	Type	Description	Example Value
TissueDiagnosisID	num	the primary key	1055
TissueTypeID	enum	The type, which will control which organ-specific fields are displayed for this tissue diagnosis	{Bladder}
BlockID *	num	The block . A block may have several tissueDiagnoses.	212
LesionLetter *	text	Each tissue diagnosis on a block gets a unique letter--A,B,C,etc.	A
OutsideTDNumber	text	The unique identifier of this tissue diagnosis at an outside institution	R4041
MicroscopistID	enum	the person who circled this tissue diagnosiis and assigned a diagnosis	{John Smith}
Area_mm2	float	The area of this tissue diagnosis. Since tissue diagnoses aren't perfect circles, this can be harder to calculate	4.0
RegionSize	float	The length of the longest line that can be drawn inside this tissue diagnosis	1.0

Users

Represents people, and includes everyone who logs onto TMAJ.

Users Table
Column Name	Type	Description	Example Value
UserID	num	the primary key for this table	51
UserName *	text	the name a user logs in with	jsmith
NameLast	text	the user's last name	Smith
NameFirst	text	the user's first name	John
Institution	text	the place where the user works	JHH
Password	text	a hash of the user's password; this column is not displayed in the JTable.	EVdCtPT724ZIVrNZXQE/PkL2ZFC=
Department	text	the department in where the user works	Pathology
Phone	text	the user's work or cell phone number	410-555-0812
Email	text	the user's email (not used)	[email protected]
AccessImportApp	bool	true if the user may access the Import application	No
AccessImagesApp	bool	true if the user may access the Images application	Yes
SpecimensApp	enum	see SpecimensApp field	{4-open}
ArrayBuilderApp	enum	see ArrayBuilderApp field	{2-read_only}
AdminApp	enum	see AdminApp field	{2-group admin}
AccessSamplesApp	bool	true if the user may access the Samples application	No
ArrayManagerApp	bool	true if the user may access the ArrayManager App	No
AccessPatientData	bool	true if the user can see the patients tab in the Specimens application. (note that you must also set a value in the client.config file as well to be able to see this tab)	No

UsersArrayBlocks

A many-to-many table that links Users to ArrayBlocks, and allows us to determine which arrayBlocks each user may access.

UsersArrayBlocks Table
Column Name	Type	Description	Example Value
ID	num	the primary key	2454
UserID *	num	any userID from the Users table	1
ArrayBlockID*	num	the arrayBlockID of an ArrayBlock to which UserID has access	3

UsersProjects

A many-to-many table that links Users to Projects, and allows us to determine which projects each user may access.

UsersProjects Table
Column Name	Type	Description	Example Value
ID	num	the primary key	5015
UserID *	num	any userID from the Users table	12
ProjectID *	num	the projectID of a project to which UserID has access	3

UsersSessions

Represents a permission that a user has to another user's session. This allows users to give other users access to their sessions.
Remember, a user automatically owns the session they create. (Note the UserID field in the sessions table.)

UsersSessions Table
Column Name	Type	Description	Example Value
ID	num	the primary key	875445
SessionID *	num	the session	25
UserID *	num	the userID of the user being given permission. (Not the User who actually owns the session.)	55
Permission	char	either r or w. r if the user can read the session; w if the user scan write it	r

UsersSpecimens

A many-to-many table that links Users to Specimens, and allows us to determine which specimens each user may access.

UsersSpecimens Table
Column Name	Type	Description	Example Value
ID	num	the primary key	43112
UserID *	num	any userID from the Users table	544
SpecimenID*	num	a specimen to which the user has access. The user may be given permission to all specimens, such that this table is irrelevant.	3

UsersUsers

A many-to-many table that links group-admin users to other users. This table determines which users a group-admin can control.

UsersUsers Table
Column Name	Type	Description	Example Value
ID	num	the primary key	412
AdminUserID *	num	a user that is a group admin. A group admin is someone who might administer the data for one lab (and the users table has users from multiple labs.)	5
UserID*	num	a user to whom the group admin may assign access privileges.	89

ArrayBuilderApp Field [Users table]

ArrayBuilderApp field options
Access Level	Description
3-Standard	Allows users to change the design of any ArrayBlocks to which they have access, unless the ArrayBlock is declared final. This is the most typical permission level for ArrayBuilder. Anyone who is designing ArrayBlocks should be given this access level.
2-Read-Only	This allows users only to view the design of their assigned ArrayBlocks. They may not make any changes to the ArrayBlocks. To this user, it would appear that every ArrayBlock they are assigned is final.
1-None	Does not allow the user to open the ArrayBlock application. A "User does not have permission to access the application" error will be given if they try to log in to ArrayBuilder.

AdminApp Field [Users table]

AdminApp field options
Access Level	Description
3-Admin	Has full access to all data that TMAJ makes available. They can create new users and assign them permissions.
2-Group-Admin	Like an administrator, but this user has only been given admin access to a subset of users, projects, array-blocks, and specimens. For example, group admins could assign a user (in their group) to an arrayblock that they have been assigned. But they couldn't do anything to a user that wasn't in their group. Nor could they give access to a resource (a project, arrayblock, or specimen) that they themselves do not have access. Group admins have access to any projects or arrayblocks that they have been assigned or that they themselves have created. Group admins have access to any specimens that they have been assigned OR that they or anyone else in their group have created.
1-None	This is the level assigned to most users. They have no administrator privileges, and must be assigned projects, arrayblocks, and specimens by an an admin or group-admin.

SpecimensApp Field [Users table]

SpecimensApp field options
Access Level	Access Application?	Make Modifications?	View All Specimens?	Description
1-None				The user will not be able to access the Specimens application. They will get an error saying "User does not have permission to access application" when they try to log in.
2-Read Only	X			Users can view (but not change) any specimens to which they have been assigned.
3-Standard	X	X		Users can add new specimens and make changes to them. This is the most typical level assigned to users. Note than whenever a user enters a new specimen, they are automatically assigned access to it.
4-Open	X	X		The same as "Standard", except for one thing. The question is what happens when a user tries to enter a new specimen that is already in TMAJ, but to which they do not have access. In Standard access, the user will be told to contact a TMAJ administrator to [[give them access to the specimen]]. In Open access, the user will automaticaly be given access to the requested specimen. This access level is basically the same as Standard, and should be given to users whom you suspect have specimens that are already entered into TMAJ by someone else. Note: Users can also quickly enter specimens, blocks, and tissue-diagnosis's in the [[lookup panel]] in the ArrayBuilder application. If a user is not assigned at least Open Access here, and they try to enter a specimen to which they do not have permission, they will get an error.
5-All	X	X	X	Users may view and change all specimens, blocks, and tissueDiagnosis's in TMAJ.