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
email	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
email	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
email	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
email	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
email	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
email	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
email	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
email	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)