Dumped on 2003-7-3.
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.
F-Key | Name | Type | Description |
---|---|---|---|
actual_input_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | NOT NULL |
public -> formal_inputs | formal_input_id | oid | NOT NULL |
public -> module_executions | input_module_execution_id | oid | NOT NULL |
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.
F-Key | Name | Type | Description |
---|---|---|---|
analysis_chain_execution_id | serial oid | NOT NULL PRIMARY KEY | |
public -> analysis_chains | analysis_chain_id | oid | NOT NULL |
public -> datasets | dataset_id | oid | NOT NULL |
public -> experimenters | experimenter_id | oid | NOT NULL |
timestamp | timestamp with time zone | default ('now'::text)::timestamp(6) with time zone |
Tables referencing this one via Foreign Key Constraints:
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.
F-Key | Name | Type | Description |
---|---|---|---|
analysis_chain_link_id | serial oid | NOT NULL PRIMARY KEY | |
public -> analysis_chains | analysis_chain_id | oid | NOT NULL |
public -> analysis_chain_nodes | from_node | oid | NOT NULL |
public -> formal_outputs | from_output | oid | NOT NULL |
public -> analysis_chain_nodes | to_node | oid | NOT NULL |
public -> formal_inputs | to_input | oid | NOT NULL |
A single node within an analysis chain. Multiple nodes in a single chain can refer to the same MODULE.
F-Key | Name | Type | Description |
---|---|---|---|
analysis_chain_node_id | serial oid | NOT NULL PRIMARY KEY | |
public -> analysis_chains | analysis_chain_id | oid | NOT NULL |
public -> modules | module_id | oid | NOT 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:
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.
F-Key | Name | Type | Description |
---|---|---|---|
analysis_chain_id | serial oid | NOT NULL PRIMARY KEY | |
public -> experimenters | owner | oid | NOT NULL |
name | character varying(64) | NOT NULL | |
description | text | ||
locked | boolean | NOT NULL default 'f'::bool |
Tables referencing this one via Foreign Key Constraints:
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.
F-Key | Name | Type | Description |
---|---|---|---|
analysis_node_execution_id | serial oid | NOT NULL PRIMARY KEY | |
public -> analysis_chain_executions | analysis_chain_execution_id | oid | NOT NULL |
public -> analysis_chain_nodes | analysis_chain_node_id | oid | NOT NULL |
public -> module_executions | module_execution_id | oid | NOT NULL |
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.
F-Key | Name | Type | Description |
---|---|---|---|
public -> analysis_paths | path_id | oid | NOT NULL |
path_order | integer | NOT NULL | |
public -> analysis_chain_nodes | analysis_chain_node_id | oid | NOT NULL |
Name | Constraint |
---|---|
analysis_path_map_pkey | PRIMARY KEY (path_id, path_order) |
F-Key | Name | Type | Description |
---|---|---|---|
path_id | serial oid | NOT NULL PRIMARY KEY | |
path_length | integer | NOT NULL | |
public -> analysis_chains | analysis_chain_id | oid | NOT NULL |
Tables referencing this one via Foreign Key Constraints:
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
type | text | ||
power | real | ||
light_source | oid |
F-Key | Name | Type | Description |
---|---|---|---|
id | integer | ||
bin | bytea |
Bounds of a feature
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
x | integer | ||
y | integer | ||
width | integer | ||
height | integer |
This describes how each channel in the pixel array relates to LogicalChannels
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
pixels_id | oid | ||
index | integer | ||
color_domain | text | ||
logical_channel | oid |
This table holds this OME instance's configuration parameters. It will normally be filled in by script or installer queries at OME install time.
F-Key | Name | Type | Description |
---|---|---|---|
configuration_id | smallint | NOT 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 |
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.
F-Key | Name | Type | Description |
---|---|---|---|
data_column_id | serial oid | NOT NULL PRIMARY KEY | |
public -> data_tables | data_table_id | oid | NOT NULL |
column_name | character varying(64) | NOT NULL | |
description | text | ||
sql_type | character varying(64) | NOT NULL | |
reference_type | character varying(64) |
Name | Constraint |
---|---|
data_columns_data_table_id_key | UNIQUE (data_table_id, column_name) |
Tables referencing this one via Foreign Key Constraints:
Each database table used to stored analysis results has an entry in the DATA_TABLES table.
F-Key | Name | Type | Description |
---|---|---|---|
data_table_id | serial oid | NOT 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 |
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:
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
F-Key | Name | Type | Description |
---|---|---|---|
dataset_id | serial oid | NOT NULL PRIMARY KEY | |
name | character varying(256) | NOT NULL | |
public -> experimenters | owner_id | oid | NOT NULL |
public -> groups | group_id | oid | |
description | text | ||
locked | boolean | NOT NULL default 'f'::bool |
Tables referencing this one via Foreign Key Constraints:
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT 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 |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
manufacturer | text | ||
model | text | ||
lot_number | text | ||
filter | oid |
A specification for displaying a logical channel
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
channel_number | integer | ||
black_level | integer | ||
white_level | integer | ||
gamma | real |
Parameters for viewers to optimally display an image
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT 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 |
A region of interest within the image for display purposes
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
x0 | integer | ||
y0 | integer | ||
z0 | integer | ||
x1 | integer | ||
y1 | integer | ||
z1 | integer | ||
t0 | integer | ||
t1 | integer | ||
display_options | oid |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
manufacturer | text | ||
model | text | ||
lot_number | text | ||
type | text | ||
filter | oid |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
manufacturer | text | ||
model | text | ||
lot_number | text | ||
type | text | ||
filter | oid |
Defines the relationship between Experimenters and Groups.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
experimenter_id | oid | ||
group_id | oid |
The experimenters table defines the people who perform imaging experiments. Each experimenter may belong to one Group
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
ome_name | character varying(30) | UNIQUE | |
firstname | character varying(30) | ||
lastname | character varying(30) | ||
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:
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
type | text | ||
description | text | ||
experimenter | oid |
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.
F-Key | Name | Type | Description |
---|---|---|---|
fullpath | character varying(255) |
Specifies information about the shape of a feature
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT 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 | real | For 2D spots, this includes fenestrations | |
perimeter | real | Outside perimeter; does not include inside perimeters in fenestrated spots | |
form_factor | real | 3D: surface area/volume; 2D: perimeter/surface area; 1.0=circle or sphere |
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.
F-Key | Name | Type | Description |
---|---|---|---|
feature_id | serial oid | NOT NULL PRIMARY KEY | |
public -> images | image_id | oid | NOT 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:
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
type | text | ||
power | real | ||
light_source | oid |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
instrument | oid |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
manufacturer | text | ||
model | text | ||
lot_number | text | ||
filter | oid |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT 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 |
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
F-Key | Name | Type | Description |
---|---|---|---|
formal_input_id | serial oid | NOT NULL PRIMARY KEY | |
public -> modules | module_id | oid | NOT NULL |
name | character varying(64) | NOT NULL | |
description | text | ||
optional | boolean | default 'f'::bool | |
list | boolean | default 't'::bool | |
public -> semantic_types | semantic_type_id | oid | NOT NULL |
public -> lookup_tables | lookup_table_id | oid | |
user_defined | boolean | default 'f'::bool |
Name | Constraint |
---|---|
formal_inputs_module_id_key | UNIQUE (module_id, name) |
Tables referencing this one via Foreign Key Constraints:
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
F-Key | Name | Type | Description |
---|---|---|---|
formal_output_id | serial oid | NOT NULL PRIMARY KEY | |
public -> modules | module_id | oid | NOT NULL |
name | character varying(64) | NOT NULL | |
description | text | ||
optional | boolean | default 'f'::bool | |
list | boolean | default 't'::bool | |
public -> semantic_types | semantic_type_id | oid | |
feature_tag | character varying(128) |
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:
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
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT 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:
This table represents the many-to-many relationship between Images and Datasets
F-Key | Name | Type | Description |
---|---|---|---|
public -> images | image_id | oid | NOT NULL |
public -> datasets | dataset_id | oid | NOT NULL |
Name | Constraint |
---|---|
image_dataset_map_pkey | PRIMARY KEY (image_id, dataset_id) |
Describes the physical size of each dimension of the pixels in an image in microns
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
pixel_size_x | real | in microns | |
pixel_size_y | real | in microns | |
pixel_size_z | real | in microns | |
pixel_size_c | real | in nanometers | |
pixel_size_t | real | in seconds |
This table will eventually contain various "hints" to a graphical image viewer.
F-Key | Name | Type | Description |
---|---|---|---|
image_display_settings_id | serial oid | NOT NULL PRIMARY KEY | |
url | text |
Tables referencing this one via Foreign Key Constraints:
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
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 |
This specifies the Experiment an Image belongs to
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
experiment | oid | ||
group_id | oid | ||
instrument | oid | ||
objective | oid |
Storage location and data type of the image pixels, including the extent of each dimension in the 5-D array.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
size_x | integer | Number of pixels on the X axis. | |
size_y | integer | Number of pixels on the Y axis. | |
size_z | integer | Number of pixels on the Z axis. | |
size_c | integer | Number of channel components in all logical channels. | |
size_t | integer | Number 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:
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
plate | oid | ||
sample | integer | ||
well | text |
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
F-Key | Name | Type | Description |
---|---|---|---|
image_type | serial oid | NOT NULL PRIMARY KEY | |
type_name | character varying(64) | ||
implementation_lang | character varying(32) | ||
classpath | character varying(255) | ||
attributes_table | character varying(64) |
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.
F-Key | Name | Type | Description |
---|---|---|---|
image_id | serial oid | NOT NULL PRIMARY KEY | |
image_guid | character varying(256) | ||
name | character varying(256) | NOT NULL | |
description | text | ||
public -> experimenters | experimenter_id | oid | NOT NULL |
public -> groups | group_id | oid | |
created | timestamp with time zone | NOT NULL | |
inserted | timestamp with time zone | NOT NULL | |
public -> image_pixels | pixels_id | oid | This is the "primary" set of pixels associated with this image. |
Tables referencing this one via Foreign Key Constraints:
Various environmental conditions at the time of image acquisition.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
temperature | real | ||
air_pressure | real | ||
humidity | real | ||
co2_percent | real |
Describes a microscope. Mainly acts as a container for the components that constitute it - e.g., Objectives, Filters, etc.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
manufacturer | text | ||
model | text | ||
serial_number | text | ||
orientation | text |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT 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 |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
manufacturer | text | ||
model | text | ||
serial_number | text | ||
instrument | oid |
Specifies a feature's 3D spatial location, in pixels
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
x | real | ||
y | real | ||
z | real |
Various pieces of information pertaining to each logical channel in an image
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT 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 |
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.
F-Key | Name | Type | Description |
---|---|---|---|
lookup_table_entry_id | serial oid | NOT NULL PRIMARY KEY | |
public -> lookup_tables | lookup_table_id | oid | NOT NULL |
value | character varying(256) | NOT NULL | |
label | character varying(256) |
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.
F-Key | Name | Type | Description |
---|---|---|---|
lookup_table_id | serial oid | NOT NULL PRIMARY KEY | |
name | character varying(64) | NOT NULL | |
description | text |
Tables referencing this one via Foreign Key Constraints:
F-Key | Name | Type | Description |
---|---|---|---|
category_id | serial oid | NOT NULL PRIMARY KEY | |
name | character varying(64) | NOT NULL | |
public -> module_categories | parent_category_id | oid | |
description | text |
Name | Constraint |
---|---|
module_catego_parent_catego_key | UNIQUE (parent_category_id, name) |
Tables referencing this one via Foreign Key Constraints:
This table defines a "run" of a particular module against a particular dataset.
F-Key | Name | Type | Description |
---|---|---|---|
module_execution_id | serial oid | NOT 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 | oid | NOT NULL |
timestamp | timestamp with time zone | default ('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) |
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:
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.
F-Key | Name | Type | Description |
---|---|---|---|
module_id | serial oid | NOT 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 | oid | Groups 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 | text | An 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:
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
manufacturer | text | ||
model | text | ||
serial_number | text | ||
lens_na | real | ||
magnification | real | ||
instrument | oid |
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.
F-Key | Name | Type | Description |
---|---|---|---|
session_id | serial oid | NOT NULL PRIMARY KEY | |
session_key | character varying(36) | ||
public -> experimenters | experimenter_id | oid | NOT 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 zone | default ('now'::text)::timestamp(6) with time zone | |
started | timestamp with time zone | default ('now'::text)::timestamp(6) with time zone |
Tables referencing this one via Foreign Key Constraints:
Multiple Images, Projects, and/or Datasets may be associated with a session. This table lists the Images associated with a particular Session.
F-Key | Name | Type | Description |
---|---|---|---|
public -> images | image_id | oid | |
public -> ome_sessions | session_id | oid |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT 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 |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT 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 |
Defines the relationship between Plates and Screens.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
plate | oid | ||
screen | oid |
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.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
name | text | ||
external_reference | text | ||
screen | oid |
This table specifies the many-to-many relationship between Datasets and Projects.
F-Key | Name | Type | Description |
---|---|---|---|
public -> projects | project_id | oid | NOT NULL |
public -> datasets | dataset_id | oid | NOT NULL |
Name | Constraint |
---|---|
project_dataset_map_pkey | PRIMARY KEY (project_id, dataset_id) |
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.
F-Key | Name | Type | Description |
---|---|---|---|
project_id | serial oid | NOT NULL PRIMARY KEY | |
name | character varying(64) | NOT NULL | |
public -> experimenters | owner_id | oid | NOT NULL |
public -> groups | group_id | oid | |
view | character varying(64) | ||
description | text |
Tables referencing this one via Foreign Key Constraints:
Ratio
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
ratio | real |
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
F-Key | Name | Type | Description |
---|---|---|---|
"path" | UNIQUE | ||
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
module_execution_id | oid | ||
path | character varying(256) | NOT NULL |
Stores information about a high-throughput screen.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
name | text | ||
description | text | ||
external_reference | text |
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
F-Key | Name | Type | Description |
---|---|---|---|
semantic_element_id | serial oid | NOT NULL PRIMARY KEY | |
public -> semantic_types | semantic_type_id | oid | NOT NULL |
name | character varying(64) | NOT NULL | |
public -> data_columns | data_column_id | oid | NOT NULL |
description | text |
Name | Constraint |
---|---|
semantic_elem_semantic_type_key | UNIQUE (semantic_type_id, name) |
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.
F-Key | Name | Type | Description |
---|---|---|---|
semantic_type_output_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | NOT NULL |
public -> semantic_types | semantic_type_id | oid | NOT NULL |
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.
F-Key | Name | Type | Description |
---|---|---|---|
semantic_type_id | serial oid | NOT 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 |
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:
Spectral information about a feature
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
the_c | integer | ||
centroid_x | real | ||
centroid_y | real | ||
centroid_z | real | ||
integral | real | ||
mean | real | ||
geomean | real | ||
sigma | real | ||
background | real |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT 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 |
Stage labels are stage coordinates and a label to recall a microscope stage location
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
name | text | ||
x | real | ||
y | real | ||
z | real |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
threshold | integer |
A thumbnail is used to display a quick small representation of the image to the user.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> images | image_id | oid | NOT NULL |
mime_type | text | ||
repository | oid | ||
path | text |
Specifies a single timepoint that this feature belongs to
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
the_t | integer |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
name | text | ||
total_distance | real | In pixels | |
average_velocity | real | In microns/second |
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> module_executions | module_execution_id | oid | |
public -> features | feature_id | oid | NOT NULL |
trajectory | oid | ||
entry_order | integer | ||
delta_x | real | In pixels | |
delta_y | real | In pixels | |
delta_z | real | In pixels | |
distance | real | In microns | |
velocity | real | In microns/second |
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.
F-Key | Name | Type | Description |
---|---|---|---|
name | character varying(32) | ||
description | text | ||
template | text | ||
type | character varying(32) |
This table stores viewer preferences for an experimenter.
F-Key | Name | Type | Description |
---|---|---|---|
attribute_id | serial oid | NOT NULL PRIMARY KEY | |
public -> experimenters | experimenter_id | oid | NOT NULL |
toolbox_scale | real |
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