Dumped on 2003-7-3.

Index of database - ome


Table: public.actual_inputs

This table stores the actual inputs that were used by a specific analysis by linking the data type declaration (FORMAL_INPUT_ID) and the MODULE_EXECUTION_ID to an INPUT_MODULE_EXECUTION_ID. All of the outputs of the INPUT_ANALYSIS, of the same type as the specified FORMAL_INPUT, are considered to be inputs of the specified ANALYSIS.

public.actual_inputs Structure
F-Key Name Type Description
actual_input_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oidNOT NULL
public -> formal_inputs formal_input_id oidNOT NULL
public -> module_executions input_module_execution_id oidNOT NULL

Index - Schema public


Table: public.analysis_chain_executions

There is exactly one row in this table for each time an analysis chain is executed against a dataset. This information cannot necessarily be reconstructed from the actual inputs and outputs and attributes, since there could be attribute reuse involved.

public.analysis_chain_executions Structure
F-Key Name Type Description
analysis_chain_execution_id serial oidNOT NULL PRIMARY KEY
public -> analysis_chains analysis_chain_id oidNOT NULL
public -> datasets dataset_id oidNOT NULL
public -> experimenters experimenter_id oidNOT NULL
timestamp timestamp with time zonedefault ('now'::text)::timestamp(6) with time zone

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.analysis_chain_links

Defines the edges in an analysis chain. Links are only allowed between modules if they connect outputs and inputs of the same type: i.e., the SEMANTIC_TYPE_ID's of the FROM_OUTPUT and TO_INPUT must match. Further, FROM_NODE and TO_NODE must be members of the same ANALYSIS_CHAIN.

public.analysis_chain_links Structure
F-Key Name Type Description
analysis_chain_link_id serial oidNOT NULL PRIMARY KEY
public -> analysis_chains analysis_chain_id oidNOT NULL
public -> analysis_chain_nodes from_node oidNOT NULL
public -> formal_outputs from_output oidNOT NULL
public -> analysis_chain_nodes to_node oidNOT NULL
public -> formal_inputs to_input oidNOT NULL

Index - Schema public


Table: public.analysis_chain_nodes

A single node within an analysis chain. Multiple nodes in a single chain can refer to the same MODULE.

public.analysis_chain_nodes Structure
F-Key Name Type Description
analysis_chain_node_id serial oidNOT NULL PRIMARY KEY
public -> analysis_chains analysis_chain_id oidNOT NULL
public -> modules module_id oidNOT NULL

The analysis module which is run at this stage of the analysis chain.
iterator_tag character varying(128)Overrides the value defined in MODULES.DEFAULT_ITERATOR_TAG. See the FEATURES table for more information.
new_feature_tag character varying(128)Overrides the value defined in MODULES.NEW_FEATURE_TAG. See the FEATURES table for more information.

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.analysis_chains

An "analysis chain" (or equivalently, "analysis view") is a directed graph of analysis modules liked via their formal inputs/outputs. It represents an execution plan for a chain of modules. Multiple instances of a given analysis module can exist in a single chain.

public.analysis_chains Structure
F-Key Name Type Description
analysis_chain_id serial oidNOT NULL PRIMARY KEY
public -> experimenters owner oidNOT NULL
name character varying(64)NOT NULL
description text
locked booleanNOT NULL default 'f'::bool

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.analysis_node_executions

This table maps rows in the MODULE_EXECUTIONS table to the nodes which executed them. Every time a node is executed in a chain, a row is created in this table, even if data reuse occurs.

public.analysis_node_executions Structure
F-Key Name Type Description
analysis_node_execution_id serial oidNOT NULL PRIMARY KEY
public -> analysis_chain_executions analysis_chain_execution_id oidNOT NULL
public -> analysis_chain_nodes analysis_chain_node_id oidNOT NULL
public -> module_executions module_execution_id oidNOT NULL

Index - Schema public


Table: public.analysis_path_map

This table links a path through a directed graph of analyses to specific analyses. Paths traverse the directed graph of analyses from the root node to a specific leaf node. There is exactly one unique path between each root node and each leaf node. Due to branching and merging in this analysis graph, analyses may belong to more than one path. A given path is composed of many analyses. This table specifies the many-to-many relationship between paths and analyses.

public.analysis_path_map Structure
F-Key Name Type Description
public -> analysis_paths path_id oidNOT NULL
path_order integerNOT NULL
public -> analysis_chain_nodes analysis_chain_node_id oidNOT NULL

 

public.analysis_path_map Constraints
Name Constraint
analysis_path_map_pkey PRIMARY KEY (path_id, path_order)

Index - Schema public


Table: public.analysis_paths

public.analysis_paths Structure
F-Key Name Type Description
path_id serial oidNOT NULL PRIMARY KEY
path_length integerNOT NULL
public -> analysis_chains analysis_chain_id oidNOT NULL

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.arcs

public.arcs Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
type text
power real
light_source oid

Index - Schema public


Table: public.bintest

public.bintest Structure
F-Key Name Type Description
id integer
bin bytea

Index - Schema public


Table: public.bounds

Bounds of a feature

public.bounds Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
x integer
y integer
width integer
height integer

Index - Schema public


Table: public.channel_components

This describes how each channel in the pixel array relates to LogicalChannels

public.channel_components Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
pixels_id oid
index integer
color_domain text
logical_channel oid

Index - Schema public


Table: public.configuration

This table holds this OME instance's configuration parameters. It will normally be filled in by script or installer queries at OME install time.

public.configuration Structure
F-Key Name Type Description
configuration_id smallintNOT NULL PRIMARY KEY default 1
mac_address character varying(20)
db_instance character(6)
lsid_authority character varying(256)
tmp_dir character varying(256)
xml_dir character varying(256)
bin_dir character varying(256)
repository_dir character varying(256)
ome_root character varying(256)
public -> modules import_module oid
public -> analysis_chains import_chain oid
public -> image_display_settings display_settings oid

Index - Schema public


Table: public.data_columns

This table stores the names of the columns in each data table. Each data table is required to declare three implicit columns, which are _not_ entered into the DATA_COLUMNS table. They are ATTRIBUTE_ID; ANALYIS_ID; and one of DATASET_ID, IMAGE_ID, and FEATURE_ID, depending on the table's granularity.

public.data_columns Structure
F-Key Name Type Description
data_column_id serial oidNOT NULL PRIMARY KEY
public -> data_tables data_table_id oidNOT NULL
column_name character varying(64)NOT NULL
description text
sql_type character varying(64)NOT NULL
reference_type character varying(64)

 

public.data_columns Constraints
Name Constraint
data_columns_data_table_id_key UNIQUE (data_table_id, column_name)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.data_tables

Each database table used to stored analysis results has an entry in the DATA_TABLES table.

public.data_tables Structure
F-Key Name Type Description
data_table_id serial oidNOT NULL PRIMARY KEY
granularity character(1)NOT NULL

The kind of attribute table being refered to is represented by a single character - G, D, I or F corresponding to Global, Dataset, Image or Feature
table_name character varying(64)NOT NULL
description text

 

public.data_tables Constraints
Name Constraint
data_tables_granularity CHECK (((granularity = 'G'::bpchar) OR (granularity = 'D'::bpchar)) OR (granularity = 'I'::bpchar)) OR (granularity = 'F'::bpchar)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.datasets

Datasets are groups of images representing a "computational unit". Once an analysis is performed on a Dataset, the LOCKED flag is set and the list of images that compose a dataset may no longer be changed. Images may belong to one or more Datasets. This many-to-many relationship is specified by the IMAGE_DATASET_MAP table

public.datasets Structure
F-Key Name Type Description
dataset_id serial oidNOT NULL PRIMARY KEY
name character varying(256)NOT NULL
public -> experimenters owner_id oidNOT NULL
public -> groups group_id oid
description text
locked booleanNOT NULL default 'f'::bool

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.detectors

public.detectors Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
serial_number text
type text
gain real
voltage real
d_offset real
instrument oid

Index - Schema public


Table: public.dichroics

public.dichroics Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
lot_number text
filter oid

Index - Schema public


Table: public.display_channels

A specification for displaying a logical channel

public.display_channels Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
channel_number integer
black_level integer
white_level integer
gamma real

Index - Schema public


Table: public.display_options

Parameters for viewers to optimally display an image

public.display_options Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
zoom real
red_channel oid
red_on boolean
green_channel oid
green_on boolean
blue_channel oid
blue_on boolean
display_rgb boolean
grey_channel oid
color_map text
z_start integer
z_stop integer
t_start integer
t_stop integer

Index - Schema public


Table: public.display_roi

A region of interest within the image for display purposes

public.display_roi Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
x0 integer
y0 integer
z0 integer
x1 integer
y1 integer
z1 integer
t0 integer
t1 integer
display_options oid

Index - Schema public


Table: public.emission_filters

public.emission_filters Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
lot_number text
type text
filter oid

Index - Schema public


Table: public.excitation_filters

public.excitation_filters Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
lot_number text
type text
filter oid

Index - Schema public


Table: public.experimenter_group_map

Defines the relationship between Experimenters and Groups.

public.experimenter_group_map Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
experimenter_id oid
group_id oid

Index - Schema public


Table: public.experimenters

The experimenters table defines the people who perform imaging experiments. Each experimenter may belong to one Group

public.experimenters Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
ome_name character varying(30)UNIQUE
firstname character varying(30)
lastname character varying(30)
email character varying(50)
password character varying(64)
group_id oid
data_dir character varying(256)
institution character varying(256)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.experiments

public.experiments Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
type text
description text
experimenter oid

Index - Schema public


Table: public.expired_files

This table keeps track of any auxiliary file used by OME that is no longer needed, but is not yet deleted from the file system.

public.expired_files Structure
F-Key Name Type Description
fullpath character varying(255)

Index - Schema public


Table: public.extent

Specifies information about the shape of a feature

public.extent Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
min_x integer
min_y integer
min_z integer
max_x integer
max_y integer
max_z integer
sigma_x integer
sigma_y integer
sigma_z integer
volume integer
surface_area realFor 2D spots, this includes fenestrations
perimeter realOutside perimeter; does not include inside perimeters in fenestrated spots
form_factor real3D: surface area/volume; 2D: perimeter/surface area; 1.0=circle or sphere

Index - Schema public


Table: public.features

The FEATURES table is used for ALL image features reguardless of algorithm. Image features are understood to be objects of interest within the image - blobs, cells, nuclei, etc. The properties of a feature are that it has a variable list of attributes. The kinds of attributes in this list and their values define everything known about the feature. Feature attribute tables contain a column named FEATURE_ID that refers to the FEATURE_ID column of this table. Algorithms that define features (segmentation algorithms) write rows into this table - one row per feature. Further, features are given tags and arranged hierarchically within an image. Modules can then request to iterate over features at an arbitrary point in the hierarchy by specifying a feature tag. This hierarchy is created automatically; new features from a module are considered to be children of the iterated feature for that module.

public.features Structure
F-Key Name Type Description
feature_id serial oidNOT NULL PRIMARY KEY
public -> images image_id oidNOT NULL
public -> features parent_feature_id oid
tag character varying(128)NOT NULL

This column is a semantic tag assigned to the feature, e.g., "CELL", "NUCLEUS", "CHROMOSOME".
name character varying(128)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.filaments

public.filaments Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
type text
power real
light_source oid

Index - Schema public


Table: public.filter

public.filter Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
instrument oid

Index - Schema public


Table: public.filter_sets

public.filter_sets Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
lot_number text
filter oid

Index - Schema public


Table: public.find_spots_inputs

public.find_spots_inputs Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
time_start integer
time_stop integer
channel integer
min_volume real
threshold_type text
threshold_value real

Index - Schema public


Table: public.formal_inputs

The FORMAL_INPUTS table declares the semantic types used as inputs by an analysis module. Each input maps to exactly one entry in the SEMANTIC_TYPES table. A table of possible user input values may be specified by referring to an entry in LOOKUP_TABLES. FORMAL_INPUTS has a many-to-one relationship with the MODULES table: A MODULE has zero or more FORMAL_INPUTS

public.formal_inputs Structure
F-Key Name Type Description
formal_input_id serial oidNOT NULL PRIMARY KEY
public -> modules module_id oidNOT NULL
name character varying(64)NOT NULL
description text
optional booleandefault 'f'::bool
list booleandefault 't'::bool
public -> semantic_types semantic_type_id oidNOT NULL
public -> lookup_tables lookup_table_id oid
user_defined booleandefault 'f'::bool

 

public.formal_inputs Constraints
Name Constraint
formal_inputs_module_id_key UNIQUE (module_id, name)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.formal_outputs

The FORMAL_OUTPUTS table declares the semantic types generated as outputs from a analysis modules. Each output maps to exactly one entry in the SEMANTIC_TYPES table. FORMAL_OUTPUTS has a many-to-one relationship with the MODULES table: A MODULE has one or more FORMAL_OUTPUTS

public.formal_outputs Structure
F-Key Name Type Description
formal_output_id serial oidNOT NULL PRIMARY KEY
public -> modules module_id oidNOT NULL
name character varying(64)NOT NULL
description text
optional booleandefault 'f'::bool
list booleandefault 't'::bool
public -> semantic_types semantic_type_id oid
feature_tag character varying(128)

 

public.formal_outputs Constraints
Name Constraint
formal_outputs_module_id_key UNIQUE (module_id, name)
formal_outputs_module_id_key1 UNIQUE (module_id, semantic_type_id)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.groups

The groups table defines groups of experimenters. This is can be a lab or project group. It is not meant to represent an institution or a company

public.groups Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
module_execution_id oid
name character varying(30)
public -> experimenters leader oid
public -> experimenters contact oid

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.image_dataset_map

This table represents the many-to-many relationship between Images and Datasets

public.image_dataset_map Structure
F-Key Name Type Description
public -> images image_id oidNOT NULL
public -> datasets dataset_id oidNOT NULL

 

public.image_dataset_map Constraints
Name Constraint
image_dataset_map_pkey PRIMARY KEY (image_id, dataset_id)

Index - Schema public


Table: public.image_dimensions

Describes the physical size of each dimension of the pixels in an image in microns

public.image_dimensions Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
pixel_size_x realin microns
pixel_size_y realin microns
pixel_size_z realin microns
pixel_size_c realin nanometers
pixel_size_t realin seconds

Index - Schema public


Table: public.image_display_settings

This table will eventually contain various "hints" to a graphical image viewer.

public.image_display_settings Structure
F-Key Name Type Description
image_display_settings_id serial oidNOT NULL PRIMARY KEY
url text

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.image_files_xyzwt

Entries in this table store locations of the non-OME image files used to constitute an OME image. Using this table, it is possible to assemble an aritrary number of images into a single 5-D OME Image

public.image_files_xyzwt Structure
F-Key Name Type Description
public -> images image_id oid
file_sha1 character(40)
bigendian boolean
path character varying(256)
host character varying(256)
url character varying(256)
x_start smallint
x_stop smallint
y_start smallint
y_stop smallint
z_start smallint
z_stop smallint
w_start smallint
w_stop smallint
t_start smallint
t_stop smallint

Index - Schema public


Table: public.image_info

This specifies the Experiment an Image belongs to

public.image_info Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
experiment oid
group_id oid
instrument oid
objective oid

Index - Schema public


Table: public.image_pixels

Storage location and data type of the image pixels, including the extent of each dimension in the 5-D array.

public.image_pixels Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
size_x integerNumber of pixels on the X axis.
size_y integerNumber of pixels on the Y axis.
size_z integerNumber of pixels on the Z axis.
size_c integerNumber of channel components in all logical channels.
size_t integerNumber of time points
bits_per_pixel integer
pixel_type text
file_sha1 text
repository oid
path text

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.image_plates

public.image_plates Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
plate oid
sample integer
well text

Index - Schema public


Table: public.image_types

This table allows OME to keep track of the formats of the non-OME image files, and the various programs used to import them into OME

public.image_types Structure
F-Key Name Type Description
image_type serial oidNOT NULL PRIMARY KEY
type_name character varying(64)
implementation_lang character varying(32)
classpath character varying(255)
attributes_table character varying(64)

Index - Schema public


Table: public.images

The Images table contains information common to all images, including both the local ID and the globally unique ID, and several references to other tables with additional image information.

public.images Structure
F-Key Name Type Description
image_id serial oidNOT NULL PRIMARY KEY
image_guid character varying(256)
name character varying(256)NOT NULL
description text
public -> experimenters experimenter_id oidNOT NULL
public -> groups group_id oid
created timestamp with time zoneNOT NULL
inserted timestamp with time zoneNOT NULL
public -> image_pixels pixels_id oidThis is the "primary" set of pixels associated with this image.

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.imaging_environments

Various environmental conditions at the time of image acquisition.

public.imaging_environments Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
temperature real
air_pressure real
humidity real
co2_percent real

Index - Schema public


Table: public.instruments

Describes a microscope. Mainly acts as a container for the components that constitute it - e.g., Objectives, Filters, etc.

public.instruments Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
serial_number text
orientation text

Index - Schema public


Table: public.lasers

public.lasers Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
type text
medium text
wavelength integer
freq_dbld boolean
tunable boolean
pulse text
power real
light_source oid
pump oid

Index - Schema public


Table: public.light_sources

public.light_sources Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
serial_number text
instrument oid

Index - Schema public


Table: public.location

Specifies a feature's 3D spatial location, in pixels

public.location Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
x real
y real
z real

Index - Schema public


Table: public.logical_channels

Various pieces of information pertaining to each logical channel in an image

public.logical_channels Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
name text
samples_per_pixel integer
filter oid
light_source oid
light_attenuation real
light_wavelength integer
otf oid
detector oid
detector_offset real
detector_gain real
illumination_type text
pinhole_size integer
photometric_interpretation text
mode text
contrast_method text
aux_light_source oid
aux_light_attenuation real
aux_technique text
aux_light_wavelength integer
ex_wave integer
em_wave integer
fluor text
nd_filter real

Index - Schema public


Table: public.lookup_table_entries

This table and LOOKUP_TABLES make up a mechanism to restrict certain module inputs to a list of values. This table identifies the values in a list, and LOOKUP_TABLES identifies the various value lists.

public.lookup_table_entries Structure
F-Key Name Type Description
lookup_table_entry_id serial oidNOT NULL PRIMARY KEY
public -> lookup_tables lookup_table_id oidNOT NULL
value character varying(256)NOT NULL
label character varying(256)

Index - Schema public


Table: public.lookup_tables

This table and LOOKUP_TABLE_ENTRIES make up a mechanism to restrict certain module inputs to a list of values. This table identifies the list, and LOOKUP_TABLE_ENTRIES identifies the values for that list.

public.lookup_tables Structure
F-Key Name Type Description
lookup_table_id serial oidNOT NULL PRIMARY KEY
name character varying(64)NOT NULL
description text

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.module_categories

public.module_categories Structure
F-Key Name Type Description
category_id serial oidNOT NULL PRIMARY KEY
name character varying(64)NOT NULL
public -> module_categories parent_category_id oid
description text

 

public.module_categories Constraints
Name Constraint
module_catego_parent_catego_key UNIQUE (parent_category_id, name)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.module_executions

This table defines a "run" of a particular module against a particular dataset.

public.module_executions Structure
F-Key Name Type Description
module_execution_id serial oidNOT NULL PRIMARY KEY
public -> modules module_id oid
dependence character(1)NOT NULL

This column specifies the highest level of the dataset-image-feature hierarchy that an analysis is dependent on. DEPENDENCE can contain a single character, G, D or I corresponding to Global, Dataset and Image.
public -> datasets dataset_id oidNOT NULL
timestamp timestamp with time zonedefault ('now'::text)::timestamp(6) with time zone
total_time double precision
attribute_sort_time double precision
attribute_db_time double precision
attribute_create_time double precision
status character varying(16)

 

public.module_executions Constraints
Name Constraint
module_executions_dependence CHECK ((dependence = 'G'::bpchar) OR (dependence = 'D'::bpchar)) OR (dependence = 'I'::bpchar)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.modules

This table specifies an analysis module registered with OME. There is only one entry in this table for each module known to OME, unlike the MODULE_EXECUTIONS table, which has one entry per module run.

public.modules Structure
F-Key Name Type Description
module_id serial oidNOT NULL PRIMARY KEY
name character varying(64)NOT NULL
description text
location character varying(128)NOT NULL

The physical location of the module. This has different meanings for different analysis handlers. For instance, the OME::Analysis::CLIHandler module type expects this field to be the filename of a command-line executable. OME::Analysis::PerlHandler expects this to be the name of a Perl class.
module_type character varying(128)NOT NULL

Specifies the analysis handler used to execute this module. Separate analysis handlers are written for each "class" of module, e.g., interal Perl script, external command-line module, external SOAP service. This field should refer to a Perl class, visible to OME, implementing the OME::Analysis::Handler interface.
public -> module_categories category oidGroups modules by category to organize things for the user.
default_iterator character varying(128)If this module takes in feature-granular inputs, this column specifies which features in the feature hierarchy are presented as inputs to the module. It can be overridden at chain-design-time via the ANALYSIS_CHAIN_NODES.ITERATOR_TAG column. For more information, see the FEATURES table.
new_feature_tag character varying(128)If new features are created by this module, they will be given a tag specified by this column. They will be children of the features specified by DEFAULT_ITERATOR. For more information, see the FEATURES table.
execution_instructions textAn XML fragment from the XML OME Module specification that describes how to execute the module. It is used to pass handler-specific parameters to the module's analysis handler.

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.objectives

public.objectives Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
manufacturer text
model text
serial_number text
lens_na real
magnification real
instrument oid

Index - Schema public


Table: public.ome_sessions

This table is used to store various information about the user's session. This session never expires, though the session_key may have a very short lifetime (minutes). When a new session_key is generated for a session, the appropriate row is updated with the new value.

public.ome_sessions Structure
F-Key Name Type Description
session_id serial oidNOT NULL PRIMARY KEY
session_key character varying(36)
public -> experimenters experimenter_id oidNOT NULL
host character varying(256)
public -> projects project_id oid
public -> datasets dataset_id oid
module_execution_id oid
image_view text
feature_view text
module_execution character varying(64)
public -> image_display_settings display_settings oid
last_access timestamp with time zonedefault ('now'::text)::timestamp(6) with time zone
started timestamp with time zonedefault ('now'::text)::timestamp(6) with time zone

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.ome_sessions_images

Multiple Images, Projects, and/or Datasets may be associated with a session. This table lists the Images associated with a particular Session.

public.ome_sessions_images Structure
F-Key Name Type Description
public -> images image_id oid
public -> ome_sessions session_id oid

Index - Schema public


Table: public.otfs

public.otfs Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
objective oid
filter oid
size_x integer
size_y integer
pixel_type text
repository oid
path text
optical_axis_average boolean
instrument oid

Index - Schema public


Table: public.plane_statistics

public.plane_statistics Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
the_z integer
the_c integer
the_t integer
mean real
geomean real
sigma real
minimum integer
maximum integer
centroid_x real
centroid_y real

Index - Schema public


Table: public.plate_screen_map

Defines the relationship between Plates and Screens.

public.plate_screen_map Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
plate oid
screen oid

Index - Schema public


Table: public.plates

Stores information about the plates that make up a high-throughput screen. Plates may belong to more than one screen, and have a many-to-many relationship to screens.

public.plates Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
name text
external_reference text
screen oid

Index - Schema public


Table: public.project_dataset_map

This table specifies the many-to-many relationship between Datasets and Projects.

public.project_dataset_map Structure
F-Key Name Type Description
public -> projects project_id oidNOT NULL
public -> datasets dataset_id oidNOT NULL

 

public.project_dataset_map Constraints
Name Constraint
project_dataset_map_pkey PRIMARY KEY (project_id, dataset_id)

Index - Schema public


Table: public.projects

A Project is simply a group of Datasets to be used as an organizational aid to the user. Datasets may belong to one or more Projects. This many-to-many relationship is specified by the PROJECT_DATASET_MAP table.

public.projects Structure
F-Key Name Type Description
project_id serial oidNOT NULL PRIMARY KEY
name character varying(64)NOT NULL
public -> experimenters owner_id oidNOT NULL
public -> groups group_id oid
view character varying(64)
description text

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.ratio

Ratio

public.ratio Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
ratio real

Index - Schema public


Table: public.repositories

OME Image pixels are stored in repository format - a 5-D pixel dump in XYZWT order. The Repositories table maintains directory paths to one or more repositories

public.repositories Structure
F-Key Name Type Description
"path" UNIQUE
attribute_id serial oidNOT NULL PRIMARY KEY
module_execution_id oid
path character varying(256)NOT NULL

Index - Schema public


Table: public.screens

Stores information about a high-throughput screen.

public.screens Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
name text
description text
external_reference text

Index - Schema public


Table: public.semantic_elements

Attribute columns are the atomic types which constitute semantic types in OME. A semantic type shares a common SEMANTIC_TYPE_ID which refers to a row in the SEMANTIC_TYPES tables. A semantic type has one row in this table for each column (atomic type) it consists of. The atomic types are specified by a DATA_COLUMN_ID refering to the DATA_COLUMNS table

public.semantic_elements Structure
F-Key Name Type Description
semantic_element_id serial oidNOT NULL PRIMARY KEY
public -> semantic_types semantic_type_id oidNOT NULL
name character varying(64)NOT NULL
public -> data_columns data_column_id oidNOT NULL
description text

 

public.semantic_elements Constraints
Name Constraint
semantic_elem_semantic_type_key UNIQUE (semantic_type_id, name)

Index - Schema public


Table: public.semantic_type_outputs

Records which semantic types a module execution creates attributes of. This allows the analysis engine to determine which semantic types were placed into untyped outputs. Only semantic types which do not have an output in the corresponding module are recorded here, to eliminate some redundancy of information stored.

public.semantic_type_outputs Structure
F-Key Name Type Description
semantic_type_output_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oidNOT NULL
public -> semantic_types semantic_type_id oidNOT NULL

Index - Schema public


Table: public.semantic_types

This table stores the semantic types known to OME. A semantic type is composed of one or more columns in a given table. Future versions may allow attribute types to span tables. Entries in SEMANTIC_ELEMENTS that share an SEMANTIC_TYPE_ID constitute a semantic type. There is one row in this table for each semantic type known to OME.

public.semantic_types Structure
F-Key Name Type Description
semantic_type_id serial oidNOT NULL PRIMARY KEY
name character varying(64)NOT NULL UNIQUE
granularity character(1)NOT NULL

This column describes the granularity of the semantic type, wether it applies Globally or to a Dataset, Image or Feature. This column must contain a single character, "G", "D", "I", or "F", and it must match the granularity specified in the DATA_TABLES that this types SEMANTIC_ELEMENTS refer to.
description text

 

public.semantic_types Constraints
Name Constraint
semantic_types_granularity CHECK (((granularity = 'G'::bpchar) OR (granularity = 'D'::bpchar)) OR (granularity = 'I'::bpchar)) OR (granularity = 'F'::bpchar)

Tables referencing this one via Foreign Key Constraints:

Index - Schema public


Table: public.signal

Spectral information about a feature

public.signal Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
the_c integer
centroid_x real
centroid_y real
centroid_z real
integral real
mean real
geomean real
sigma real
background real

Index - Schema public


Table: public.stack_statistics

public.stack_statistics Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
the_c integer
the_t integer
mean real
geomean real
sigma real
minimum integer
maximum integer
centroid_x real
centroid_y real
centroid_z real

Index - Schema public


Table: public.stage_labels

Stage labels are stage coordinates and a label to recall a microscope stage location

public.stage_labels Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
name text
x real
y real
z real

Index - Schema public


Table: public.threshold

public.threshold Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
threshold integer

Index - Schema public


Table: public.thumbnails

A thumbnail is used to display a quick small representation of the image to the user.

public.thumbnails Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> images image_id oidNOT NULL
mime_type text
repository oid
path text

Index - Schema public


Table: public.timepoint

Specifies a single timepoint that this feature belongs to

public.timepoint Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
the_t integer

Index - Schema public


Table: public.trajectory

public.trajectory Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
name text
total_distance realIn pixels
average_velocity realIn microns/second

Index - Schema public


Table: public.trajectory_entry

public.trajectory_entry Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> module_executions module_execution_id oid
public -> features feature_id oidNOT NULL
trajectory oid
entry_order integer
delta_x realIn pixels
delta_y realIn pixels
delta_z realIn pixels
distance realIn microns
velocity realIn microns/second

Index - Schema public


Table: public.view_templates

This table is used to store SQL templates for generating views. The SQL is stored in the template column and may include variables in the form $(VariableName) that will be substituted by the apropriate value when the view is created. Commonly used variables include $(ExperimenterID), $(ImageID), $(ProjectID), $(DatasetID), etc.

public.view_templates Structure
F-Key Name Type Description
name character varying(32)
description text
template text
type character varying(32)

Index - Schema public


Table: public.viewer_preferences

This table stores viewer preferences for an experimenter.

public.viewer_preferences Structure
F-Key Name Type Description
attribute_id serial oidNOT NULL PRIMARY KEY
public -> experimenters experimenter_id oidNOT NULL
toolbox_scale real

Index - Schema public


Function: public.oid( bigint )

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