Table controlled_vocab_values | |||
---|---|---|---|
* | vocab_value_id | bigserial | |
* | controlled_vocab_id | bigint | |
* | term | varchar | |
* | order_by | varchar | |
default_item | varchar | ||
Indexes | |||
Pk | pk_controlled_vocab_values | 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 | |||
---|---|---|---|
Overarching investigation information.An investigation comprises one or more individual studies. | |||
* | investigation_id | bigserial | |
* | name | varchar | |
* | description | varchar | Describes the overarching goal of the investigation |
contact_person_id | bigint | ||
Indexes | |||
Pk | pk_investigation | 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 investigation_study | |||
---|---|---|---|
* | investigation_id | bigint | |
* | study_id | bigint | |
Indexes | |||
Pk | idx_investigation_study | 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 study_experimental_factor | |||
---|---|---|---|
EFO ontological link of experimental factors to studies | |||
* | study_id | bigint | |
* | efo_id | bigint | |
Indexes | |||
Pk | idx_study_experimental_factor | 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 | |
* | pmid | varchar | |
Indexes | |||
Pk | idx_study_pmid | ON study_id, pmid | |
idx_study_pmid_0 | ON study_id | ||
Foreign Keys | |||
fk_study_pmid_study | ( study_id ) ref study (study_id) |
Table job_results_filepath | |||
---|---|---|---|
Holds connection between jobs and the result filepaths | |||
* | job_id | bigint | |
* | filepath_id | bigint | |
Indexes | |||
Pk | idx_job_results_filepath | 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 | Id of the analysis |
* | job_id | bigint | Id for a job that is part of the analysis |
Indexes | |||
Pk | idx_analysis_jobs | 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 | |
* | child_id | bigint | |
Indexes | |||
idx_analysis_chain | ON parent_id | ||
idx_analysis_chain_0 | ON child_id | ||
Pk | idx_analysis_chain_1 | 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 | |
* | column_name | varchar | |
Indexes | |||
Pk | idx_column_controlled_vocabularies | 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 | |
* | data_type | varchar | |
* | desc_or_value | varchar | |
* | definition | varchar | |
min_length | integer | ||
* | active | integer | |
Indexes | |||
Pk | pk_mixs_field_description | ON column_name |
Table analysis_users | |||
---|---|---|---|
Links analyses to the users they are shared with | |||
* | analysis_id | bigint | |
* | varchar | ||
Indexes | |||
Pk | idx_analysis_users | 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 | |
* | preprocessed_data_id | bigint | |
Indexes | |||
Pk | idx_study_preprocessed_data | 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 | |
* | varchar | ||
Indexes | |||
Pk | idx_study_users | 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 | |
* | description | varchar | |
other_mapping_columns | varchar | Represents whatever other columns go with this study | |
Indexes | |||
Pk | pk_study_x_y | ON sample_id |
Table study_sample_columns | |||
---|---|---|---|
Holds information on which metadata columns are available for the study sample template | |||
* | study_id | bigint | |
* | column_name | varchar( 100 ) | |
* | column_type | varchar | |
Indexes | |||
Pk | idx_study_mapping_columns | 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 study_raw_data | |||
---|---|---|---|
links study to its raw data | |||
* | study_id | bigint | |
* | raw_data_id | bigint | |
Indexes | |||
idx_study_raw_data | ON study_id | ||
Pk | idx_study_raw_data_0 | 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 portal_type | |||
---|---|---|---|
What portals are available to show a study in | |||
* | portal_type_id | bigserial | |
* | portal | varchar | |
* | description | varchar | |
Indexes | |||
Pk | pk_portal_type | ON portal_type_id |
Table processed_filepath | |||
---|---|---|---|
* | processed_data_id | bigint | |
* | filepath_id | bigint | |
Indexes | |||
Pk | idx_processed_filepath | 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 | Unique identifier for function |
* | name | varchar | |
* | command | varchar | What command to call to run this function |
* | input | varchar | JSON of input options for the command |
* | required | varchar | JSON of required options for the command |
* | optional | varchar | JSON of optional options for command |
* | output | varchar | JSON of output options for the command |
Indexes | |||
Pk | pk_command | ON command_id |
Table logging | |||
---|---|---|---|
* | logging_id | bigserial | |
* | time | timestamp | Time the error was thrown |
* | severity_id | integer | |
* | msg | varchar | Error message thrown |
information | varchar | Other applicable information (depending on error) | |
Indexes | |||
idx_logging_0 | ON severity_id | ||
Pk | pk_logging | ON logging_id | |
Foreign Keys | |||
fk_logging_severity | ( severity_id ) ref severity (severity_id) |
Table study_processed_data | |||
---|---|---|---|
* | study_id | bigint | |
* | processed_data_id | bigint | |
Indexes | |||
Pk | idx_study_processed_data | ON study_id, processed_data_id | |
idx_study_processed_data_0 | ON study_id | ||
U | pk_study_processed_data | 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 | |
* | data_type_id | bigint | |
Indexes | |||
Pk | idx_command_data_type | 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 | |
* | filepath_id | bigint | |
Indexes | |||
Pk | idx_preprocessed_filepath | 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 | |
* | filepath_id | bigint | |
data_type_id | bigint | ||
Indexes | |||
idx_analysis_filepath | ON analysis_id | ||
idx_analysis_filepath_0 | ON filepath_id | ||
Pk | idx_analysis_filepath_1 | 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 | |
* | step | integer | |
Indexes | |||
Pk | pk_analysis_workflow | 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 | |
* | ontology_short_name | varchar | |
* | bioportal_id | integer | |
ontology_branch_id | varchar | ||
Indexes | |||
Pk | idx_column_ontology | 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 | |
* | name | varchar | |
* | varchar | ||
* | affiliation | varchar | The institution with which this person is affiliated |
address | varchar( 100 ) | ||
phone | varchar | ||
Indexes | |||
Pk | pk_study_person | ON study_person_id | |
U | idx_study_person | ON name, affiliation |
Table analysis | |||
---|---|---|---|
hHolds analysis information | |||
* | analysis_id | bigserial | Unique identifier for analysis |
* | varchar | Email for user who owns the analysis | |
* | name | varchar | Name of the analysis |
* | description | varchar | |
* | analysis_status_id | bigint | |
pmid | varchar | PMID of paper from the analysis | |
timestamp | timestamptz DEFO current_timestamp | ||
Indexes | |||
Pk | pk_analysis | 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 controlled_vocab | |||
---|---|---|---|
* | controlled_vocab_id | bigserial | |
* | controlled_vocab | varchar | |
Indexes | |||
Pk | pk_controlled_vocabularies | ON controlled_vocab_id |
Table ontology | |||
---|---|---|---|
* | ontology_id | bigint | |
* | ontology | varchar | |
* | fully_loaded | bool | |
fullname | varchar | ||
query_url | varchar | ||
source_url | varchar | ||
definition | text | ||
* | load_date | date | |
Indexes | |||
Pk | pk_ontology | ON ontology_id | |
U | idx_ontology | ON ontology |
Table preprocessed_sequence_454_params | |||
---|---|---|---|
Parameters used for processing sequence data. | |||
* | preprocessed_params_id | bigserial | |
* | trim_length | integer | |
Indexes | |||
Pk | pk_preprocessed_sequence_454_params | ON preprocessed_params_id |
Table preprocessed_spectra_params | |||
---|---|---|---|
Parameters used for processing spectra data. | |||
* | preprocessed_params_id | bigserial | |
col | varchar | ||
Indexes | |||
Pk | pk_preprocessed_spectra_params | ON preprocessed_params_id |
Table reference | |||
---|---|---|---|
* | reference_id | bigserial | |
* | reference_name | varchar | |
reference_version | varchar | ||
* | sequence_filepath | bigint | |
taxonomy_filepath | bigint | ||
tree_filepath | bigint | ||
Indexes | |||
Pk | pk_reference | 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 processed_params_uclust | |||
---|---|---|---|
Parameters used for processing data using method uclust | |||
* | processed_params_id | bigserial | |
* | reference_id | bigint | What version of reference or type of reference used |
* | similarity | float8 DEFO 0.97 | |
* | enable_rev_strand_match | bool DEFO TRUE | |
* | suppress_new_clusters | bool DEFO TRUE | |
Indexes | |||
Pk | pk_processed_params_uclust | ON processed_params_id | |
idx_processed_params_uclust | ON reference_id | ||
Foreign Keys | |||
fk_processed_params_uclust | ( reference_id ) ref reference (reference_id) |
Table processed_params_sortmerna | |||
---|---|---|---|
Parameters used for processing data using method sortmerna | |||
* | processed_params_id | bigserial | |
* | reference_id | bigint | What version of reference or type of reference used |
* | evalue | float8 | |
* | max_pos | integer | |
* | similarity | float8 | |
* | coverage | float8 | |
* | threads | integer | |
Indexes | |||
Pk | pk_processed_params_sortmerna | ON processed_params_id | |
idx_processed_params_sortmerna | ON reference_id | ||
Foreign Keys | |||
fk_processed_params_sortmerna | ( reference_id ) ref reference (reference_id) |
Table preprocessed_sequence_illumina_params | |||
---|---|---|---|
Parameters used for processing illumina sequence data. | |||
* | preprocessed_params_id | bigserial | |
* | max_bad_run_length | integer DEFO 3 | |
* | min_per_read_length_fraction | real DEFO 0.75 | |
* | sequence_max_n | integer DEFO 0 | |
* | rev_comp_barcode | bool DEFO FALSE | |
* | rev_comp_mapping_barcodes | bool DEFO FALSE | |
* | rev_comp | bool DEFO FALSE | |
* | phred_quality_threshold | integer DEFO 3 | |
* | barcode_type | varchar DEFO 'golay_12' | |
* | max_barcode_errors | real DEFO 1.5 | |
Indexes | |||
Pk | pk_preprocessed_sequence_illumina_params | ON preprocessed_params_id |
Table preprocessed_processed_data | |||
---|---|---|---|
* | preprocessed_data_id | bigint | |
* | processed_data_id | bigint | |
Indexes | |||
Pk | idx_preprocessed_processed_data | 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 study | |||
---|---|---|---|
* | study_id | bigserial | Unique name for study |
* | varchar | Email of study owner | |
* | study_status_id | bigint | |
emp_person_id | bigint | ||
* | first_contact | timestamp DEFO current_timestamp | |
funding | varchar | ||
* | timeseries_type_id | bigint | What type of timeseries this study is (or is not) Controlled Vocabulary |
lab_person_id | bigint | ||
* | metadata_complete | bool | |
* | mixs_compliant | bool | |
most_recent_contact | timestamp | ||
number_samples_collected | integer | ||
number_samples_promised | integer | ||
* | portal_type_id | bigint | |
* | principal_investigator_id | bigint | |
* | reprocess | bool | |
spatial_series | bool | ||
* | study_title | varchar | |
* | study_alias | varchar | |
* | study_description | text | |
* | study_abstract | text | |
vamps_id | varchar | ||
Indexes | |||
Pk | pk_study | ON study_id | |
idx_study | ON email | ||
idx_study_0 | ON study_status_id | ||
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 | ||
U | unique_study_title | ON study_title | |
Foreign Keys | |||
fk_study_user | ( email ) ref qiita_user (email) | ||
fk_study_study_status | ( study_status_id ) ref study_status (study_status_id) | ||
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 qiita_user | |||
---|---|---|---|
Holds all user information | |||
* | varchar | ||
* | user_level_id | integer DEFO 5 | user level |
* | password | varchar | |
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 | pk_user | 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 | |
data | bigint | STUFFFFF | |
Indexes | |||
Pk | pk_prep_y | ON sample_id |
Table prep_columns | |||
---|---|---|---|
* | prep_template_id | bigint | |
* | column_name | varchar | |
* | column_type | varchar | |
Indexes | |||
Pk | idx_prep_columns_0 | 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 | |
* | filepath_id | bigint | |
Indexes | |||
Pk | idx_raw_filepath | 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 emp_status | |||
---|---|---|---|
All possible statuses for projects relating to EMP. Whether they are part of, processed in accordance to, or not part of EMP. | |||
* | emp_status_id | bigserial | |
* | emp_status | varchar | |
Indexes | |||
Pk | pk_emp_status | ON emp_status_id | |
U | idx_emp_status | ON emp_status |
Table required_sample_info_status | |||
---|---|---|---|
* | required_sample_info_status_id | bigserial | |
status | varchar | ||
Indexes | |||
Pk | pk_sample_status | ON required_sample_info_status_id | |
U | idx_required_sample_info_status | ON status |
Table study_status | |||
---|---|---|---|
* | study_status_id | bigserial | |
* | status | varchar | |
* | description | varchar | |
Indexes | |||
Pk | pk_study_status | ON study_status_id | |
U | idx_study_status | ON status |
Table filetype | |||
---|---|---|---|
Type of file (FASTA, FASTQ, SPECTRA, etc) | |||
* | filetype_id | bigserial | |
* | type | varchar | |
Indexes | |||
Pk | pk_filetype | ON filetype_id | |
U | idx_filetype | ON type |
Table filepath_type | |||
---|---|---|---|
* | filepath_type_id | bigserial | |
filepath_type | varchar | ||
Indexes | |||
Pk | pk_filepath_type | ON filepath_type_id | |
U | idx_filepath_type | ON filepath_type |
Table checksum_algorithm | |||
---|---|---|---|
* | checksum_algorithm_id | bigserial | |
* | name | varchar | |
Indexes | |||
Pk | pk_checksum_algorithm | ON checksum_algorithm_id | |
U | idx_checksum_algorithm | ON name |
Table data_type | |||
---|---|---|---|
* | data_type_id | bigserial | |
* | data_type | varchar | Data type (16S, metabolome, etc) the job will use |
Indexes | |||
Pk | pk_data_type | ON data_type_id | |
U | idx_data_type | ON data_type |
Table user_level | |||
---|---|---|---|
Holds available user levels | |||
* | user_level_id | serial | |
* | name | varchar | One of the user levels (admin, user, guest, etc) |
* | description | text | |
Indexes | |||
Pk | pk_user_level | ON user_level_id | |
U | idx_user_level | ON name |
Table analysis_status | |||
---|---|---|---|
* | analysis_status_id | bigserial | |
* | status | varchar | |
Indexes | |||
Pk | pk_analysis_status | ON analysis_status_id | |
U | idx_analysis_status | ON status |
Table job_status | |||
---|---|---|---|
* | job_status_id | bigserial | |
* | status | varchar | |
Indexes | |||
Pk | pk_job_status | ON job_status_id | |
U | idx_job_status_0 | ON status |
Table severity | |||
---|---|---|---|
* | severity_id | serial | |
* | severity | varchar | |
Indexes | |||
Pk | pk_severity | ON severity_id | |
U | idx_severity | ON severity |
Table prep_template | |||
---|---|---|---|
* | prep_template_id | bigserial | |
* | data_type_id | bigint | |
* | raw_data_id | bigint | |
* | preprocessing_status | varchar DEFO 'not_preprocessed' | |
investigation_type | varchar | The investigation type (e.g., one of the values from EBI's set of known types) | |
Indexes | |||
Pk | pk_prep_template | 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 | |
* | filetype_id | bigint | |
* | link_filepaths_status | varchar DEFO 'idle' | |
Indexes | |||
U | pk_raw_data | ON raw_data_id | |
idx_raw_data | ON filetype_id | ||
Pk | pk_raw_data_0 | ON raw_data_id | |
Foreign Keys | |||
fk_raw_data_filetype | ( filetype_id ) ref filetype (filetype_id) |
Table preprocessed_data | |||
---|---|---|---|
* | preprocessed_data_id | bigserial | |
* | preprocessed_params_table | varchar | Name of table holding the params |
* | preprocessed_params_id | bigint | |
* | submitted_to_insdc_status | varchar DEFO 'not submitted' | |
ebi_submission_accession | varchar | ||
ebi_study_accession | varchar | ||
* | data_type_id | bigint | |
* | link_filepaths_status | varchar DEFO 'idle' | |
Indexes | |||
Pk | pk_preprocessed_data | 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 processed_data | |||
---|---|---|---|
* | processed_data_id | bigserial | |
* | processed_params_table | varchar | Name of table holding processing params |
* | processed_params_id | bigint | Link to a table with the parameters used to generate processed data |
* | processed_date | timestamp | |
* | data_type_id | bigint | |
* | link_filepaths_status | varchar DEFO 'idle' | |
Indexes | |||
Pk | pk_processed_data | ON processed_data_id | |
idx_processed_data | ON data_type_id | ||
Foreign Keys | |||
fk_processed_data | ( data_type_id ) ref data_type (data_type_id) |
Table job | |||
---|---|---|---|
* | job_id | bigserial | Unique identifier for job |
* | data_type_id | bigint | What datatype (16s, metabolome, etc) job is run on. |
* | job_status_id | bigint | |
* | command_id | bigint | 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 | pk_job | 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 | |
* | filepath | varchar | |
* | filepath_type_id | bigint | |
* | checksum | varchar | |
* | checksum_algorithm_id | bigint | |
data_directory_id | bigserial | ||
Indexes | |||
Pk | pk_filepath | 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 | |
* | data_type | varchar | |
* | mountpoint | varchar | |
* | subdirectory | varchar | |
* | active | bool | |
Indexes | |||
Pk | pk_data_directory | ON data_directory_id |
Table term | |||
---|---|---|---|
* | term_id | bigserial | |
* | ontology_id | bigint | |
old_term_id | bigint DEFO NULL | Identifier used in the old system, we are keeping this for consistency | |
* | term | varchar | |
identifier | varchar | ||
definition | varchar | ||
namespace | varchar | ||
is_obsolete | bool DEFO 'false' | ||
is_root_term | bool | ||
is_leaf | bool | ||
* | user_defined | bool DEFO False | Whether or not this term was defined by a user |
Indexes | |||
Pk | pk_term | ON term_id | |
idx_term | ON ontology_id | ||
Foreign Keys | |||
fk_term_ontology | ( ontology_id ) ref ontology (ontology_id) |
Table common_prep_info | |||
---|---|---|---|
* | prep_template_id | bigint | The prep template identifier |
* | sample_id | varchar | |
center_name | varchar | ||
center_project_name | varchar | ||
* | emp_status_id | bigint | |
Indexes | |||
idx_required_prep_info_0 | ON emp_status_id | ||
idx_required_prep_info_2 | ON sample_id | ||
idx_common_prep_info_0 | ON sample_id | ||
Pk | idx_common_prep_info | ON prep_template_id, sample_id | |
idx_common_prep_info_1 | ON prep_template_id | ||
Foreign Keys | |||
fk_required_prep_info_emp_status | ( emp_status_id ) ref emp_status (emp_status_id) | ||
fk_common_prep_info | ( sample_id ) ref required_sample_info (sample_id) | ||
fk_prep_template | ( prep_template_id ) ref prep_template (prep_template_id) |
Table analysis_sample | |||
---|---|---|---|
* | analysis_id | bigint | |
* | processed_data_id | bigint | |
* | sample_id | varchar | |
Indexes | |||
idx_analysis_sample | ON analysis_id | ||
idx_analysis_sample_0 | ON processed_data_id | ||
idx_analysis_sample_1 | ON 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 required_sample_info (sample_id) |
Table environmental_package | |||
---|---|---|---|
* | environmental_package_name | varchar | The name of the environmental package |
* | metadata_table | varchar | Contains the name of the table that contains the pre-defined metadata columns for the environmental package |
Indexes | |||
Pk | pk_environmental_package | ON environmental_package_name |
Table study_environmental_package | |||
---|---|---|---|
Holds the 1 to many relationship between the study and the environmental_package | |||
* | study_id | bigint | |
* | environmental_package_name | varchar | |
Indexes | |||
Pk | pk_study_environmental_package | 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 | |
* | timeseries_type | varchar | |
* | intervention_type | varchar DEFO 'None' | |
Indexes | |||
Pk | pk_timeseries_type | ON timeseries_type_id | |
U | idx_timeseries_type | ON timeseries_type, intervention_type |
Table prep_template_filepath | |||
---|---|---|---|
* | prep_template_id | bigint | |
* | filepath_id | bigint | |
Indexes | |||
Pk | idx_prep_template_filepath | 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 required_sample_info | |||
---|---|---|---|
Required info for each sample. One row is one sample. | |||
* | sample_id | varchar | |
* | study_id | bigint | |
* | physical_location | varchar | Where the sample itself is stored |
* | has_physical_specimen | bool | Whether we have the full speciment or just DNA |
* | has_extracted_data | bool | |
* | sample_type | varchar | Controlled vocabulary of sample types |
* | required_sample_info_status_id | bigint | What step of the pipeline the samples are in |
* | collection_timestamp | timestamp | |
* | host_subject_id | varchar | |
* | description | varchar | |
* | latitude | float8 | Latitude of the collection site |
* | longitude | float8 | Longitude of the collection site |
Indexes | |||
idx_required_sample_info_0 | ON required_sample_info_status_id | ||
idx_required_sample_info | ON study_id | ||
Pk | idx_required_sample_info_1 | ON sample_id | |
Foreign Keys | |||
fk_required_sample_info | ( required_sample_info_status_id ) ref required_sample_info_status (required_sample_info_status_id) | ||
fk_required_sample_info_study | ( study_id ) ref study (study_id) |
Table sample_template_filepath | |||
---|---|---|---|
* | study_id | bigint | |
* | filepath_id | bigint | |
Indexes | |||
Pk | idx_sample_template_filepath | 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 | |
* | preprocessed_data_id | bigint | |
Indexes | |||
Pk | idx_prep_template_preprocessed_data | 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) |