Table controlled_vocab_values | ||
---|---|---|
vocab_value_id | bigserial NOT NULL | |
controlled_vocab_id | bigint NOT NULL | |
term | varchar NOT NULL | |
order_by | varchar NOT NULL | |
default_item | varchar | |
Indexes | ||
pk_controlled_vocab_values primary key | ON vocab_value_id | |
idx_controlled_vocab_values | ON controlled_vocab_id | |
Foreign Keys | ||
fk_controlled_vocab_values | ( controlled_vocab_id ) ref controlled_vocab (controlled_vocab_id) |
Table investigation_study | ||
---|---|---|
investigation_id | bigint NOT NULL | |
study_id | bigint NOT NULL | |
Indexes | ||
idx_investigation_study primary key | ON investigation_id, study_id | |
idx_investigation_study_investigation | ON investigation_id | |
idx_investigation_study_study | ON study_id | |
Foreign Keys | ||
fk_investigation_study | ( investigation_id ) ref investigation (investigation_id) | |
fk_investigation_study_study | ( study_id ) ref study (study_id) |
Table job_results_filepath | ||
---|---|---|
Holds connection between jobs and the result filepaths | ||
job_id | bigint NOT NULL | |
filepath_id | bigint NOT NULL | |
Indexes | ||
idx_job_results_filepath primary key | ON job_id, filepath_id | |
idx_job_results_filepath_0 | ON job_id | |
idx_job_results_filepath_1 | ON filepath_id | |
Foreign Keys | ||
fk_job_results_filepath | ( job_id ) ref job (job_id) | |
fk_job_results_filepath_0 | ( filepath_id ) ref filepath (filepath_id) |
Table analysis_job | ||
---|---|---|
Holds information for a one-to-many relation of analysis to the jobs in it | ||
analysis_id | bigint NOT NULL | Id of the analysis |
job_id | bigint NOT NULL | Id for a job that is part of the analysis |
Indexes | ||
idx_analysis_jobs primary key | ON analysis_id, job_id | |
idx_analysis_job | ON analysis_id | |
idx_analysis_job_0 | ON job_id | |
Foreign Keys | ||
fk_analysis_job_analysis | ( analysis_id ) ref analysis (analysis_id) | |
fk_analysis_job_job | ( job_id ) ref job (job_id) |
Table analysis_chain | ||
---|---|---|
Keeps track of the chain of analysis edits. Tracks what previous analysis a given analysis came from.If a given analysis is not in child_id, it is the root of the chain. | ||
parent_id | bigint NOT NULL | |
child_id | bigint NOT NULL | |
Indexes | ||
idx_analysis_chain | ON parent_id | |
idx_analysis_chain_0 | ON child_id | |
idx_analysis_chain_1 primary key | ON parent_id, child_id | |
Foreign Keys | ||
fk_analysis_chain | ( parent_id ) ref analysis (analysis_id) | |
fk_analysis_chain_0 | ( child_id ) ref analysis (analysis_id) |
Table column_controlled_vocabularies | ||
---|---|---|
Table relates a column with a controlled vocabulary. | ||
controlled_vocab_id | bigserial NOT NULL | |
column_name | varchar NOT NULL | |
Indexes | ||
idx_column_controlled_vocabularies primary key | ON controlled_vocab_id, column_name | |
idx_column_controlled_vocabularies_0 | ON column_name | |
idx_column_controlled_vocabularies_1 | ON controlled_vocab_id | |
Foreign Keys | ||
fk_column_controlled_vocabularies | ( column_name ) ref mixs_field_description (column_name) | |
fk_column_controlled_vocab2 | ( controlled_vocab_id ) ref controlled_vocab (controlled_vocab_id) |
Table mixs_field_description | ||
---|---|---|
column_name | varchar NOT NULL | |
data_type | varchar NOT NULL | |
desc_or_value | varchar NOT NULL | |
definition | varchar NOT NULL | |
min_length | integer | |
active | integer NOT NULL | |
Indexes | ||
pk_mixs_field_description primary key | ON column_name |
Table analysis_users | ||
---|---|---|
Links analyses to the users they are shared with | ||
analysis_id | bigint NOT NULL | |
varchar NOT NULL | ||
Indexes | ||
idx_analysis_users primary key | ON analysis_id, email | |
idx_analysis_users_analysis | ON analysis_id | |
idx_analysis_users_email | ON email | |
Foreign Keys | ||
fk_analysis_users_analysis | ( analysis_id ) ref analysis (analysis_id) | |
fk_analysis_users_user | ( email ) ref qiita_user (email) |
Table study_preprocessed_data | ||
---|---|---|
study_id | bigint NOT NULL | |
preprocessed_data_id | bigint NOT NULL | |
Indexes | ||
idx_study_preprocessed_data primary key | ON study_id, preprocessed_data_id | |
idx_study_preprocessed_data_0 | ON study_id | |
idx_study_preprocessed_data_1 | ON preprocessed_data_id | |
Foreign Keys | ||
fk_study_preprocessed_data | ( study_id ) ref study (study_id) | |
fk_study_preprocessed_data_0 | ( preprocessed_data_id ) ref preprocessed_data (preprocessed_data_id) |
Table study_users | ||
---|---|---|
Links shared studies to users they are shared with | ||
study_id | bigint NOT NULL | |
varchar NOT NULL | ||
Indexes | ||
idx_study_users primary key | ON study_id, email | |
idx_study_users_0 | ON study_id | |
idx_study_users_1 | ON email | |
Foreign Keys | ||
fk_study_users_study | ( study_id ) ref study (study_id) | |
fk_study_users_user | ( email ) ref qiita_user (email) |
Table sample_x | ||
---|---|---|
data for samples in study x (sample template)x is the study_id from study tableMAKE SURE sample_id IS FK TO sample_id IN required_sample_info TABLE | ||
sample_id | varchar NOT NULL | |
description | varchar NOT NULL | |
other_mapping_columns | varchar | Represents whatever other columns go with this study |
Indexes | ||
pk_study_x_y primary key | ON sample_id |
Table study_raw_data | ||
---|---|---|
links study to its raw data | ||
study_id | bigint NOT NULL | |
raw_data_id | bigint NOT NULL | |
Indexes | ||
idx_study_raw_data | ON study_id | |
idx_study_raw_data_0 primary key | ON study_id, raw_data_id | |
Foreign Keys | ||
fk_study_raw_data_study | ( study_id ) ref study (study_id) | |
fk_study_raw_data_raw_data | ( raw_data_id ) ref raw_data (raw_data_id) |
Table processed_filepath | ||
---|---|---|
processed_data_id | bigint NOT NULL | |
filepath_id | bigint NOT NULL | |
Indexes | ||
idx_processed_filepath primary key | ON processed_data_id, filepath_id | |
Foreign Keys | ||
fk_processed_data_filepath | ( processed_data_id ) ref processed_data (processed_data_id) | |
fk_processed_data_filepath_0 | ( filepath_id ) ref filepath (filepath_id) |
Table command | ||
---|---|---|
Available commands for jobs | ||
command_id | bigserial NOT NULL | Unique identifier for function |
name | varchar NOT NULL | |
command | varchar NOT NULL | What command to call to run this function |
input | varchar NOT NULL | JSON of input options for the command |
required | varchar NOT NULL | JSON of required options for the command |
optional | varchar NOT NULL | JSON of optional options for command |
output | varchar NOT NULL | JSON of output options for the command |
Indexes | ||
pk_command primary key | ON command_id |
Table logging | ||
---|---|---|
logging_id | bigserial NOT NULL | |
time | timestamp NOT NULL | Time the error was thrown |
severity_id | integer NOT NULL | |
msg | varchar NOT NULL | Error message thrown |
information | varchar | Other applicable information (depending on error) |
Indexes | ||
idx_logging_0 | ON severity_id | |
pk_logging primary key | ON logging_id | |
Foreign Keys | ||
fk_logging_severity | ( severity_id ) ref severity (severity_id) |
Table study_processed_data | ||
---|---|---|
study_id | bigint NOT NULL | |
processed_data_id | bigint NOT NULL | |
Indexes | ||
idx_study_processed_data primary key | ON study_id, processed_data_id | |
idx_study_processed_data_0 | ON study_id | |
pk_study_processed_data unique | ON processed_data_id | |
Foreign Keys | ||
fk_study_processed_data | ( study_id ) ref study (study_id) | |
fk_study_processed_data_0 | ( processed_data_id ) ref processed_data (processed_data_id) |
Table command_data_type | ||
---|---|---|
command_id | bigint NOT NULL | |
data_type_id | bigint NOT NULL | |
Indexes | ||
idx_command_data_type primary key | ON command_id, data_type_id | |
idx_command_data_type_0 | ON command_id | |
idx_command_data_type_1 | ON data_type_id | |
Foreign Keys | ||
fk_command_data_type | ( command_id ) ref command (command_id) | |
fk_command_data_type_0 | ( data_type_id ) ref data_type (data_type_id) |
Table preprocessed_filepath | ||
---|---|---|
preprocessed_data_id | bigint NOT NULL | |
filepath_id | bigint NOT NULL | |
Indexes | ||
idx_preprocessed_filepath primary key | ON preprocessed_data_id, filepath_id | |
idx_preprocessed_filepath_0 | ON preprocessed_data_id | |
idx_preprocessed_filepath_1 | ON filepath_id | |
Foreign Keys | ||
fk_preprocessed_filepath | ( preprocessed_data_id ) ref preprocessed_data (preprocessed_data_id) | |
fk_preprocessed_filepath_0 | ( filepath_id ) ref filepath (filepath_id) |
Table analysis_filepath | ||
---|---|---|
Stores link between analysis and the data file used for the analysis. | ||
analysis_id | bigint NOT NULL | |
filepath_id | bigint NOT NULL | |
data_type_id | bigint | |
Indexes | ||
idx_analysis_filepath | ON analysis_id | |
idx_analysis_filepath_0 | ON filepath_id | |
idx_analysis_filepath_1 primary key | ON analysis_id, filepath_id | |
idx_analysis_filepath_2 | ON data_type_id | |
Foreign Keys | ||
fk_analysis_filepath | ( analysis_id ) ref analysis (analysis_id) | |
fk_analysis_filepath_0 | ( filepath_id ) ref filepath (filepath_id) | |
fk_analysis_filepath_1 | ( data_type_id ) ref data_type (data_type_id) |
Table analysis_workflow | ||
---|---|---|
Stores what step in_production analyses are on. | ||
analysis_id | bigint NOT NULL | |
step | integer NOT NULL | |
Indexes | ||
pk_analysis_workflow primary key | ON analysis_id | |
Foreign Keys | ||
fk_analysis_workflow | ( analysis_id ) ref analysis (analysis_id) |
Table column_ontology | ||
---|---|---|
This table relates a column with an ontology. | ||
column_name | varchar NOT NULL | |
ontology_short_name | varchar NOT NULL | |
bioportal_id | integer NOT NULL | |
ontology_branch_id | varchar | |
Indexes | ||
idx_column_ontology primary key | ON column_name, ontology_short_name | |
idx_column_ontology_0 | ON column_name | |
Foreign Keys | ||
fk_column_ontology | ( column_name ) ref mixs_field_description (column_name) |
Table study_person | ||
---|---|---|
Contact information for the various people involved in a study | ||
study_person_id | bigserial NOT NULL | |
name | varchar NOT NULL | |
varchar NOT NULL | ||
affiliation | varchar NOT NULL | The institution with which this person is affiliated |
address | varchar( 100 ) | |
phone | varchar | |
Indexes | ||
pk_study_person primary key | ON study_person_id | |
idx_study_person unique | ON name, affiliation |
Table controlled_vocab | ||
---|---|---|
controlled_vocab_id | bigserial NOT NULL | |
controlled_vocab | varchar NOT NULL | |
Indexes | ||
pk_controlled_vocabularies primary key | ON controlled_vocab_id |
Table ontology | ||
---|---|---|
ontology_id | bigint NOT NULL | |
ontology | varchar NOT NULL | |
fully_loaded | bool NOT NULL | |
fullname | varchar | |
query_url | varchar | |
source_url | varchar | |
definition | text | |
load_date | date NOT NULL | |
Indexes | ||
pk_ontology primary key | ON ontology_id | |
idx_ontology unique | ON ontology |
Table preprocessed_spectra_params | ||
---|---|---|
Parameters used for processing spectra data. | ||
preprocessed_params_id | bigserial NOT NULL | |
col | varchar | |
Indexes | ||
pk_preprocessed_spectra_params primary key | ON preprocessed_params_id |
Table processed_params_uclust | ||
---|---|---|
Parameters used for processing data using method uclust | ||
processed_params_id | bigserial NOT NULL | |
reference_id | bigint NOT NULL | What version of reference or type of reference used |
similarity | float8 NOT NULL DEFO 0.97 | |
enable_rev_strand_match | bool NOT NULL DEFO TRUE | |
suppress_new_clusters | bool NOT NULL DEFO TRUE | |
Indexes | ||
pk_processed_params_uclust primary key | ON processed_params_id | |
idx_processed_params_uclust | ON reference_id | |
Foreign Keys | ||
fk_processed_params_uclust | ( reference_id ) ref reference (reference_id) |
Table preprocessed_processed_data | ||
---|---|---|
preprocessed_data_id | bigint NOT NULL | |
processed_data_id | bigint NOT NULL | |
Indexes | ||
idx_preprocessed_processed_data primary key | ON preprocessed_data_id, processed_data_id | |
idx_preprocessed_processed_data_0 | ON preprocessed_data_id | |
idx_preprocessed_processed_data_1 | ON processed_data_id | |
Foreign Keys | ||
fk_preprocessed_processed_data | ( preprocessed_data_id ) ref preprocessed_data (preprocessed_data_id) | |
fk_preprocessed_processed_data_0 | ( processed_data_id ) ref processed_data (processed_data_id) |
Table qiita_user | ||
---|---|---|
Holds all user information | ||
varchar NOT NULL | ||
user_level_id | integer NOT NULL DEFO 5 | user level |
password | varchar NOT NULL | |
name | varchar | |
affiliation | varchar | |
address | varchar | |
phone | varchar | |
user_verify_code | varchar | Code for initial user email verification |
pass_reset_code | varchar | Randomly generated code for password reset |
pass_reset_timestamp | timestamp | Time the reset code was generated |
Indexes | ||
pk_user primary key | ON email | |
idx_user | ON user_level_id | |
Foreign Keys | ||
fk_user_user_level | ( user_level_id ) ref user_level (user_level_id) |
Table prep_y | ||
---|---|---|
Information on how raw data y was prepared (prep template)Linked by y being raw_data_id from raw data table. | ||
sample_id | varchar NOT NULL | |
data | bigint | STUFFFFF |
Indexes | ||
pk_prep_y primary key | ON sample_id |
Table prep_columns | ||
---|---|---|
prep_template_id | bigint NOT NULL | |
column_name | varchar NOT NULL | |
column_type | varchar NOT NULL | |
Indexes | ||
idx_prep_columns_0 primary key | ON prep_template_id, column_name, column_type | |
idx_prep_columns_1 | ON prep_template_id | |
Foreign Keys | ||
fk_prep_columns_prep_template | ( prep_template_id ) ref prep_template (prep_template_id) |
Table raw_filepath | ||
---|---|---|
raw_data_id | bigint NOT NULL | |
filepath_id | bigint NOT NULL | |
Indexes | ||
idx_raw_filepath primary key | ON raw_data_id, filepath_id | |
idx_raw_filepath_0 | ON filepath_id | |
idx_raw_filepath_1 | ON raw_data_id | |
Foreign Keys | ||
fk_raw_filepath | ( filepath_id ) ref filepath (filepath_id) | |
fk_raw_filepath_0 | ( raw_data_id ) ref raw_data (raw_data_id) |
Table filetype | ||
---|---|---|
Type of file (FASTA, FASTQ, SPECTRA, etc) | ||
filetype_id | bigserial NOT NULL | |
type | varchar NOT NULL | |
Indexes | ||
pk_filetype primary key | ON filetype_id | |
idx_filetype unique | ON type |
Table filepath_type | ||
---|---|---|
filepath_type_id | bigserial NOT NULL | |
filepath_type | varchar | |
Indexes | ||
pk_filepath_type primary key | ON filepath_type_id | |
idx_filepath_type unique | ON filepath_type |
Table checksum_algorithm | ||
---|---|---|
checksum_algorithm_id | bigserial NOT NULL | |
name | varchar NOT NULL | |
Indexes | ||
pk_checksum_algorithm primary key | ON checksum_algorithm_id | |
idx_checksum_algorithm unique | ON name |
Table data_type | ||
---|---|---|
data_type_id | bigserial NOT NULL | |
data_type | varchar NOT NULL | Data type (16S, metabolome, etc) the job will use |
Indexes | ||
pk_data_type primary key | ON data_type_id | |
idx_data_type unique | ON data_type |
Table user_level | ||
---|---|---|
Holds available user levels | ||
user_level_id | serial NOT NULL | |
name | varchar NOT NULL | One of the user levels (admin, user, guest, etc) |
description | text NOT NULL | |
Indexes | ||
pk_user_level primary key | ON user_level_id | |
idx_user_level unique | ON name |
Table job_status | ||
---|---|---|
job_status_id | bigserial NOT NULL | |
status | varchar NOT NULL | |
Indexes | ||
pk_job_status primary key | ON job_status_id | |
idx_job_status_0 unique | ON status |
Table severity | ||
---|---|---|
severity_id | serial NOT NULL | |
severity | varchar NOT NULL | |
Indexes | ||
pk_severity primary key | ON severity_id | |
idx_severity unique | ON severity |
Table prep_template | ||
---|---|---|
prep_template_id | bigserial NOT NULL | |
data_type_id | bigint NOT NULL | |
raw_data_id | bigint NOT NULL | |
preprocessing_status | varchar NOT NULL DEFO 'not_preprocessed' | |
investigation_type | varchar | The investigation type (e.g., one of the values from EBI's set of known types) |
Indexes | ||
pk_prep_template primary key | ON prep_template_id | |
idx_prep_template | ON data_type_id | |
idx_prep_template_0 | ON raw_data_id | |
Foreign Keys | ||
fk_prep_template_data_type | ( data_type_id ) ref data_type (data_type_id) | |
fk_prep_template_raw_data | ( raw_data_id ) ref raw_data (raw_data_id) |
Table raw_data | ||
---|---|---|
raw_data_id | bigserial NOT NULL | |
filetype_id | bigint NOT NULL | |
link_filepaths_status | varchar NOT NULL DEFO 'idle' | |
Indexes | ||
pk_raw_data unique | ON raw_data_id | |
idx_raw_data | ON filetype_id | |
pk_raw_data_0 primary key | ON raw_data_id | |
Foreign Keys | ||
fk_raw_data_filetype | ( filetype_id ) ref filetype (filetype_id) |
Table job | ||
---|---|---|
job_id | bigserial NOT NULL | Unique identifier for job |
data_type_id | bigint NOT NULL | What datatype (16s, metabolome, etc) job is run on. |
job_status_id | bigint NOT NULL | |
command_id | bigint NOT NULL | The Qiime or other function being run (alpha diversity, etc) |
options | varchar | Holds all options set for the job as a json string |
log_id | bigint | Reference to error if status is error |
Indexes | ||
pk_job primary key | ON job_id | |
idx_job_command | ON command_id | |
idx_job_status | ON job_status_id | |
idx_job_type | ON data_type_id | |
idx_job | ON log_id | |
Foreign Keys | ||
fk_job_function | ( command_id ) ref command (command_id) | |
fk_job_job_status_id | ( job_status_id ) ref job_status (job_status_id) | |
fk_job_data_type | ( data_type_id ) ref data_type (data_type_id) | |
fk_job | ( log_id ) ref logging (logging_id) |
Table filepath | ||
---|---|---|
filepath_id | bigserial NOT NULL | |
filepath | varchar NOT NULL | |
filepath_type_id | bigint NOT NULL | |
checksum | varchar NOT NULL | |
checksum_algorithm_id | bigint NOT NULL | |
data_directory_id | bigserial | |
Indexes | ||
pk_filepath primary key | ON filepath_id | |
idx_filepath | ON filepath_type_id | |
idx_filepath_0 | ON data_directory_id | |
Foreign Keys | ||
fk_filepath | ( filepath_type_id ) ref filepath_type (filepath_type_id) | |
fk_filepath_0 | ( checksum_algorithm_id ) ref checksum_algorithm (checksum_algorithm_id) | |
fk_filepath_data_directory | ( data_directory_id ) ref data_directory (data_directory_id) |
Table data_directory | ||
---|---|---|
data_directory_id | bigserial NOT NULL | |
data_type | varchar NOT NULL | |
mountpoint | varchar NOT NULL | |
subdirectory | varchar NOT NULL | |
active | bool NOT NULL | |
Indexes | ||
pk_data_directory primary key | ON data_directory_id |
Table term | ||
---|---|---|
term_id | bigserial NOT NULL | |
ontology_id | bigint NOT NULL | |
old_term_id | bigint DEFO NULL | Identifier used in the old system, we are keeping this for consistency |
term | varchar NOT NULL | |
identifier | varchar | |
definition | varchar | |
namespace | varchar | |
is_obsolete | bool DEFO 'false' | |
is_root_term | bool | |
is_leaf | bool | |
user_defined | bool NOT NULL DEFO False | Whether or not this term was defined by a user |
Indexes | ||
pk_term primary key | ON term_id | |
idx_term | ON ontology_id | |
Foreign Keys | ||
fk_term_ontology | ( ontology_id ) ref ontology (ontology_id) |
Table environmental_package | ||
---|---|---|
environmental_package_name | varchar NOT NULL | The name of the environmental package |
metadata_table | varchar NOT NULL | Contains the name of the table that contains the pre-defined metadata columns for the environmental package |
Indexes | ||
pk_environmental_package primary key | ON environmental_package_name |
Table study_environmental_package | ||
---|---|---|
Holds the 1 to many relationship between the study and the environmental_package | ||
study_id | bigint NOT NULL | |
environmental_package_name | varchar NOT NULL | |
Indexes | ||
pk_study_environmental_package primary key | ON study_id, environmental_package_name | |
idx_study_environmental_package | ON study_id | |
idx_study_environmental_package_0 | ON environmental_package_name | |
Foreign Keys | ||
fk_study_environmental_package | ( study_id ) ref study (study_id) | |
fk_study_environmental_package_0 | ( environmental_package_name ) ref environmental_package (environmental_package_name) |
Table timeseries_type | ||
---|---|---|
timeseries_type_id | bigserial NOT NULL | |
timeseries_type | varchar NOT NULL | |
intervention_type | varchar NOT NULL DEFO 'None' | |
Indexes | ||
pk_timeseries_type primary key | ON timeseries_type_id | |
idx_timeseries_type unique | ON timeseries_type, intervention_type |
Table prep_template_filepath | ||
---|---|---|
prep_template_id | bigint NOT NULL | |
filepath_id | bigint NOT NULL | |
Indexes | ||
idx_prep_template_filepath primary key | ON prep_template_id, filepath_id | |
idx_prep_template_filepath | ON filepath_id | |
idx_prep_template_filepath | ON prep_template_id | |
Foreign Keys | ||
fk_filepath_id | ( filepath_id ) ref filepath (filepath_id) | |
fk_prep_template_id | ( prep_template_id ) ref prep_template (prep_template_id) |
Table sample_template_filepath | ||
---|---|---|
study_id | bigint NOT NULL | |
filepath_id | bigint NOT NULL | |
Indexes | ||
idx_sample_template_filepath primary key | ON study_id, filepath_id | |
idx_sample_template_filepath_0 | ON study_id | |
idx_sample_template_filepath_1 | ON filepath_id | |
Foreign Keys | ||
fk_study_id | ( study_id ) ref study (study_id) | |
fk_filepath_id | ( filepath_id ) ref filepath (filepath_id) |
Table prep_template_preprocessed_data | ||
---|---|---|
prep_template_id | bigint NOT NULL | |
preprocessed_data_id | bigint NOT NULL | |
Indexes | ||
idx_prep_template_preprocessed_data primary key | ON prep_template_id, preprocessed_data_id | |
idx_prep_template_preprocessed_data_0 | ON prep_template_id | |
idx_prep_template_preprocessed_data_1 | ON preprocessed_data_id | |
Foreign Keys | ||
fk_prep_template_id | ( prep_template_id ) ref prep_template (prep_template_id) | |
fk_prep_template_preprocessed_data | ( preprocessed_data_id ) ref preprocessed_data (preprocessed_data_id) |
Table preprocessed_data | ||
---|---|---|
preprocessed_data_id | bigserial NOT NULL | |
preprocessed_params_table | varchar NOT NULL | Name of table holding the params |
preprocessed_params_id | bigint NOT NULL | |
submitted_to_insdc_status | varchar NOT NULL DEFO 'not submitted' | |
ebi_submission_accession | varchar | |
ebi_study_accession | varchar | |
data_type_id | bigint NOT NULL | |
link_filepaths_status | varchar NOT NULL DEFO 'idle' | |
submitted_to_vamps_status | varchar DEFO 'not submitted' | |
processing_status | varchar NOT NULL DEFO 'not_processed' | |
Indexes | ||
pk_preprocessed_data primary key | ON preprocessed_data_id | |
idx_preprocessed_data | ON data_type_id | |
Foreign Keys | ||
fk_preprocessed_data | ( data_type_id ) ref data_type (data_type_id) |
Table reference | ||
---|---|---|
reference_id | bigserial NOT NULL | |
reference_name | varchar NOT NULL | |
reference_version | varchar | |
sequence_filepath | bigint NOT NULL | |
taxonomy_filepath | bigint | |
tree_filepath | bigint | |
Indexes | ||
pk_reference primary key | ON reference_id | |
idx_reference | ON sequence_filepath | |
idx_reference_0 | ON taxonomy_filepath | |
idx_reference_1 | ON tree_filepath | |
Foreign Keys | ||
fk_reference_sequence_filepath | ( sequence_filepath ) ref filepath (filepath_id) | |
fk_reference_taxonomy_filepath | ( taxonomy_filepath ) ref filepath (filepath_id) | |
fk_reference_tree_filepath | ( tree_filepath ) ref filepath (filepath_id) |
Table preprocessed_sequence_454_params | ||
---|---|---|
Parameters used for processing sequence data. | ||
preprocessed_params_id | bigserial NOT NULL | |
param_set_name | varchar( 100 ) NOT NULL | The name of the parameter set |
min_seq_len | integer NOT NULL DEFO 200 | The minimum sequence length |
max_seq_len | integer NOT NULL DEFO 1000 | The maximum sequence length |
trim_seq_length | bool NOT NULL DEFO f | Whether to trim the sequence length or not |
min_qual_score | integer NOT NULL DEFO 25 | The minimum phred quality score |
max_ambig | integer NOT NULL DEFO 6 | The maximum number of ambiguous characters |
max_homopolymer | integer NOT NULL DEFO 6 | The maximum homopolymer run |
max_primer_mismatch | integer NOT NULL DEFO 0 | Maximum number of mismatches to the primer allowed |
barcode_type | varchar NOT NULL DEFO 'golay_12' | The barcode type used |
max_barcode_errors | real NOT NULL DEFO 1.5 | The maximum number of allowed barcode errors |
disable_bc_correction | bool NOT NULL DEFO f | Disable barcode correction |
qual_score_window | integer NOT NULL DEFO 0 | Enable a sliding window quality score threshold, this is the size of the window |
disable_primers | bool NOT NULL DEFO f | Disable primer checking |
reverse_primers | varchar NOT NULL DEFO 'disable' | Check for reverse primers |
reverse_primer_mismatches | integer NOT NULL DEFO 0 | The number of allowed mismatches in the reverse primer |
truncate_ambig_bases_bool | bool NOT NULL DEFO f | Truncate at the first ambiguous base |
Indexes | ||
pk_preprocessed_sequence_454_params primary key | ON preprocessed_params_id |
Table preprocessed_sequence_illumina_params | ||
---|---|---|
Parameters used for processing illumina sequence data. | ||
preprocessed_params_id | bigserial NOT NULL | |
max_bad_run_length | integer NOT NULL DEFO 3 | |
min_per_read_length_fraction | real NOT NULL DEFO 0.75 | |
sequence_max_n | integer NOT NULL DEFO 0 | |
rev_comp_barcode | bool NOT NULL DEFO FALSE | |
rev_comp_mapping_barcodes | bool NOT NULL DEFO FALSE | |
rev_comp | bool NOT NULL DEFO FALSE | |
phred_quality_threshold | integer NOT NULL DEFO 3 | |
barcode_type | varchar NOT NULL DEFO 'golay_12' | |
max_barcode_errors | real NOT NULL DEFO 1.5 | |
param_set_name | varchar( 100 ) NOT NULL | The name of the parameter set |
Indexes | ||
pk_preprocessed_sequence_illumina_params primary key | ON preprocessed_params_id |
Table processed_params_sortmerna | ||
---|---|---|
Parameters used for processing data using method sortmerna | ||
processed_params_id | bigserial NOT NULL | |
reference_id | bigint NOT NULL | What version of reference or type of reference used |
sortmerna_e_value | float8 NOT NULL | |
sortmerna_max_pos | integer NOT NULL | |
similarity | float8 NOT NULL | |
sortmerna_coverage | float8 NOT NULL | |
threads | integer NOT NULL | |
param_set_name | varchar( 100 ) NOT NULL DEFO 'Default' | The name of the parameter set |
Indexes | ||
pk_processed_params_sortmerna primary key | ON processed_params_id | |
idx_processed_params_sortmerna | ON reference_id | |
Foreign Keys | ||
fk_processed_params_sortmerna | ( reference_id ) ref reference (reference_id) |
Table analysis_status | ||
---|---|---|
analysis_status_id | bigserial NOT NULL | |
status | varchar NOT NULL | |
Indexes | ||
pk_analysis_status primary key | ON analysis_status_id | |
idx_analysis_status unique | ON status |
Table collection_job | ||
---|---|---|
Matches collection important jobs as one to many. | ||
collection_id | bigint NOT NULL | |
job_id | bigint NOT NULL | |
Indexes | ||
idx_collection_job | ON collection_id | |
idx_collection_job_0 | ON job_id | |
idx_collection_job_1 primary key | ON collection_id, job_id | |
Foreign Keys | ||
fk_collection_job | ( collection_id ) ref collection (collection_id) | |
fk_collection_job_0 | ( job_id ) ref job (job_id) |
Table collection_analysis | ||
---|---|---|
Matches collection to analyses as one to many. | ||
collection_id | bigint NOT NULL | |
analysis_id | bigint NOT NULL | |
Indexes | ||
idx_collection_analysis primary key | ON collection_id, analysis_id | |
idx_collection_analysis_0 | ON collection_id | |
idx_collection_analysis_1 | ON analysis_id | |
Foreign Keys | ||
fk_collection_analysis | ( collection_id ) ref collection (collection_id) | |
fk_collection_analysis_0 | ( analysis_id ) ref analysis (analysis_id) |
Table collection_status | ||
---|---|---|
collection_status_id | bigserial NOT NULL | |
status | varchar( 1 ) NOT NULL | |
Indexes | ||
pk_collection_status primary key | ON collection_status_id |
Table collection | ||
---|---|---|
Tracks a group of analyses and important jobs for an overarching goal. | ||
collection_id | bigserial NOT NULL | |
varchar NOT NULL | ||
name | varchar( 100 ) NOT NULL | |
description | varchar | |
collection_status_id | bigint NOT NULL DEFO 1 | |
Indexes | ||
pk_collection primary key | ON collection_id | |
idx_collection | ON email | |
idx_collection_0 | ON collection_status_id | |
Foreign Keys | ||
fk_collection | ( email ) ref qiita_user (email) | |
fk_collection_0 | ( collection_status_id ) ref collection_status (collection_status_id) |
Table collection_users | ||
---|---|---|
Allows sharing of a collection | ||
collection_id | bigint NOT NULL | |
varchar NOT NULL | ||
Indexes | ||
idx_collection_user primary key | ON collection_id, email | |
idx_collection_user_0 | ON collection_id | |
idx_collection_user_1 | ON email | |
Foreign Keys | ||
fk_collection_user | ( collection_id ) ref collection (collection_id) | |
fk_collection_user_email | ( email ) ref qiita_user (email) |
Table study_sample_columns | ||
---|---|---|
Holds information on which metadata columns are available for the study sample template | ||
study_id | bigint NOT NULL | |
column_name | varchar NOT NULL | |
column_type | varchar NOT NULL | |
Indexes | ||
idx_study_mapping_columns primary key | ON study_id, column_name, column_type | |
idx_study_mapping_columns_study_id | ON study_id | |
Foreign Keys | ||
fk_study_mapping_columns_study | ( study_id ) ref study (study_id) |
Table analysis | ||
---|---|---|
hHolds analysis information | ||
analysis_id | bigserial NOT NULL | Unique identifier for analysis |
varchar NOT NULL | Email for user who owns the analysis | |
name | varchar NOT NULL | Name of the analysis |
description | varchar NOT NULL | |
analysis_status_id | bigint NOT NULL | |
pmid | varchar | PMID of paper from the analysis |
timestamp | timestamptz DEFO current_timestamp | |
dflt | bool NOT NULL DEFO false | |
Indexes | ||
pk_analysis primary key | ON analysis_id | |
idx_analysis_email | ON email | |
idx_analysis_status_id | ON analysis_status_id | |
Foreign Keys | ||
fk_analysis_user | ( email ) ref qiita_user (email) | |
fk_analysis_analysis_status | ( analysis_status_id ) ref analysis_status (analysis_status_id) |
Table study_experimental_factor | ||
---|---|---|
EFO ontological link of experimental factors to studies | ||
study_id | bigint NOT NULL | |
efo_id | bigint NOT NULL | |
Indexes | ||
idx_study_experimental_factor primary key | ON study_id, efo_id | |
idx_study_experimental_factor_0 | ON study_id | |
Foreign Keys | ||
fk_study_experimental_factor | ( study_id ) ref study (study_id) |
Table study_pmid | ||
---|---|---|
Links a study to all PMIDs for papers created from study | ||
study_id | bigint NOT NULL | |
pmid | varchar NOT NULL | |
Indexes | ||
idx_study_pmid primary key | ON study_id, pmid | |
idx_study_pmid_0 | ON study_id | |
Foreign Keys | ||
fk_study_pmid_study | ( study_id ) ref study (study_id) |
Table study | ||
---|---|---|
study_id | bigserial NOT NULL | Unique name for study |
varchar NOT NULL | Email of study owner | |
emp_person_id | bigint | |
first_contact | timestamp NOT NULL DEFO current_timestamp | |
funding | varchar | |
timeseries_type_id | bigint NOT NULL | What type of timeseries this study is (or is not) Controlled Vocabulary |
lab_person_id | bigint | |
metadata_complete | bool NOT NULL | |
mixs_compliant | bool NOT NULL | |
most_recent_contact | timestamp | |
number_samples_collected | integer | |
number_samples_promised | integer | |
portal_type_id | bigint NOT NULL | |
principal_investigator_id | bigint NOT NULL | |
reprocess | bool NOT NULL | |
spatial_series | bool | |
study_title | varchar NOT NULL | |
study_alias | varchar NOT NULL | |
study_description | text NOT NULL | |
study_abstract | text NOT NULL | |
vamps_id | varchar | |
Indexes | ||
pk_study primary key | ON study_id | |
idx_study | ON email | |
idx_study_1 | ON emp_person_id | |
idx_study_2 | ON lab_person_id | |
idx_study_3 | ON principal_investigator_id | |
idx_study_4 | ON timeseries_type_id | |
idx_study_5 | ON portal_type_id | |
unique_study_title unique | ON study_title | |
Foreign Keys | ||
fk_study_user | ( email ) ref qiita_user (email) | |
fk_study_study_emp_person | ( emp_person_id ) ref study_person (study_person_id) | |
fk_study_study_lab_person | ( lab_person_id ) ref study_person (study_person_id) | |
fk_study_study_pi_person | ( principal_investigator_id ) ref study_person (study_person_id) | |
fk_study_timeseries_type | ( timeseries_type_id ) ref timeseries_type (timeseries_type_id) | |
fk_study | ( portal_type_id ) ref portal_type (portal_type_id) |
Table processed_data | ||
---|---|---|
processed_data_id | bigserial NOT NULL | |
processed_params_table | varchar NOT NULL | Name of table holding processing params |
processed_params_id | bigint NOT NULL | Link to a table with the parameters used to generate processed data |
processed_date | timestamp NOT NULL | |
data_type_id | bigint NOT NULL | |
link_filepaths_status | varchar NOT NULL DEFO 'idle' | |
processed_data_status_id | bigint NOT NULL DEFO 4 | |
Indexes | ||
pk_processed_data primary key | ON processed_data_id | |
idx_processed_data | ON data_type_id | |
idx_processed_data_0 | ON processed_data_status_id | |
Foreign Keys | ||
fk_processed_data | ( data_type_id ) ref data_type (data_type_id) | |
fk_processed_data_status | ( processed_data_status_id ) ref processed_data_status (processed_data_status_id) |
Table investigation | ||
---|---|---|
Overarching investigation information.An investigation comprises one or more individual studies. | ||
investigation_id | bigserial NOT NULL | |
investigation_name | varchar NOT NULL | |
investigation_description | varchar NOT NULL | Describes the overarching goal of the investigation |
contact_person_id | bigint | |
Indexes | ||
pk_investigation primary key | ON investigation_id | |
idx_investigation | ON contact_person_id | |
Foreign Keys | ||
fk_investigation_study_person | ( contact_person_id ) ref study_person (study_person_id) |
Table processed_data_status | ||
---|---|---|
processed_data_status_id | bigserial NOT NULL | |
processed_data_status | varchar NOT NULL | |
processed_data_status_description | varchar NOT NULL | |
Indexes | ||
pk_study_status primary key | ON processed_data_status_id | |
idx_study_status unique | ON processed_data_status |
Table portal_type | ||
---|---|---|
What portals are available to show a study in | ||
portal_type_id | bigserial NOT NULL | |
portal | varchar NOT NULL | |
portal_description | varchar NOT NULL | |
Indexes | ||
pk_portal_type primary key | ON portal_type_id |
Table analysis_sample | ||
---|---|---|
analysis_id | bigint NOT NULL | |
processed_data_id | bigint NOT NULL | |
sample_id | varchar NOT NULL | |
Indexes | ||
idx_analysis_sample | ON analysis_id | |
idx_analysis_sample_0 | ON processed_data_id | |
idx_analysis_sample_1 | ON sample_id | |
pk_analysis_sample primary key | ON analysis_id, processed_data_id, sample_id | |
Foreign Keys | ||
fk_analysis_sample_analysis | ( analysis_id ) ref analysis (analysis_id) | |
fk_analysis_processed_data | ( processed_data_id ) ref processed_data (processed_data_id) | |
fk_analysis_sample | ( sample_id ) ref study_sample (sample_id) |
Table study_sample | ||
---|---|---|
Required info for each sample. One row is one sample. | ||
sample_id | varchar NOT NULL | |
study_id | bigint NOT NULL | |
Indexes | ||
idx_required_sample_info | ON study_id | |
idx_required_sample_info_1 primary key | ON sample_id | |
Foreign Keys | ||
fk_required_sample_info_study | ( study_id ) ref study (study_id) |
Table prep_template_sample | ||
---|---|---|
prep_template_id | bigint NOT NULL | The prep template identifier |
sample_id | varchar NOT NULL | |
Indexes | ||
idx_required_prep_info_2 | ON sample_id | |
idx_common_prep_info_0 | ON sample_id | |
idx_common_prep_info primary key | ON prep_template_id, sample_id | |
idx_common_prep_info_1 | ON prep_template_id | |
Foreign Keys | ||
fk_common_prep_info | ( sample_id ) ref study_sample (sample_id) | |
fk_prep_template | ( prep_template_id ) ref prep_template (prep_template_id) |